lots of changes for merge

81 files changed, 252 insertions, 12836 deletions

diff --git a/.gitignore b/.gitignore
index bebedfe..fb544d9 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,5 +1,3 @@
-bin/*
-obj/*
 data/raw/*
 data/raw
-makefile_*
+build/*
diff --git a/CMakeLists.txt b/CMakeLists.txt
new file mode 100644
index 0000000..ade950f
--- /dev/null
+++ b/CMakeLists.txt
@@ -0,0 +1,20 @@
+
+cmake_minimum_required(VERSION 3.5)
+project(fracture)
+
+include_directories(src ~/.local/include /usr/include/suitesparse)
+link_directories(~/.local/lib)
+
+file(GLOB LIB_SOURCES lib/*.c)
+
+add_library(fracture_stuff ${LIB_SOURCES})
+
+file(GLOB EXE_SOURCES src/*.c)
+
+foreach( src_file ${EXE_SOURCES} )
+  string( REGEX REPLACE ".*/src/(.*)\.c" "\\1" exe_name ${src_file} )
+  add_executable( ${exe_name} ${src_file} )
+  target_link_libraries(${exe_name} fracture_stuff gsl c cblas lapack dl pthread cholmod amd colamd suitesparseconfig camd ccolamd rt metis m jst tcmalloc profiler)
+  install(TARGETS ${exe_name} DESTINATION bin)
+endforeach( src_file ${EXE_SOURCES} )
+
diff --git a/data/anal.sh b/data/anal.sh
deleted file mode 100755
index 62806d0..0000000
--- a/data/anal.sh
+++ /dev/null
@@ -1,21 +0,0 @@
-anal_process avln_s_o_v_t_*
-anal_process avln_v_o_v_t_*
-anal_process avln_v_d_v_t_*
-anal_process cstr_s_o_v_t_*
-anal_process cstr_v_o_v_t_*
-anal_process cstr_v_d_v_t_*
-cen_anal_process damg_s_o_v_t_*
-cen_anal_process damg_v_o_v_t_*
-cen_anal_process damg_v_d_v_t_*
-big_anal_process cond_s_o_v_t_*
-big_anal_process cond_v_o_v_t_*
-big_anal_process cond_v_d_v_t_*
-long_anal_process strs_s_o_v_t_*
-long_anal_process strs_v_o_v_t_*
-long_anal_process strs_v_d_v_t_*
-long_anal_process thrs_s_o_v_t_*
-long_anal_process thrs_v_o_v_t_*
-long_anal_process thrs_v_d_v_t_*
-long_anal_process enrg_s_o_v_t_*
-long_anal_process enrg_v_o_v_t_*
-long_anal_process enrg_v_d_v_t_*
diff --git a/data/anal_p.sh b/data/anal_p.sh
deleted file mode 100755
index ac33bc1..0000000
--- a/data/anal_p.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-../../bin/anal_process avln_b_s_o_c_c_*
-../../bin/anal_process cstr_b_s_o_c_c_*
-../../bin/cen_anal_process damg_b_s_o_c_c_*
-../../bin/big_anal_process cond_b_s_o_c_c_*
-../../bin/long_anal_process strs_b_s_o_c_c_*
-../../bin/long_anal_process enrg_b_s_o_c_c_*
diff --git a/data/anal_t.sh b/data/anal_t.sh
deleted file mode 100755
index e7f137b..0000000
--- a/data/anal_t.sh
+++ /dev/null
@@ -1,24 +0,0 @@
-anal_process avln_s_o_v_t_*
-anal_process avln_v_o_v_t_*
-anal_process avln_v_d_v_t_*
-anal_process cstr_s_o_v_t_*
-anal_process cstr_v_o_v_t_*
-anal_process cstr_v_d_v_t_*
-cen_anal_process damg_s_o_v_t_*
-cen_anal_process damg_v_o_v_t_*
-cen_anal_process damg_v_d_v_t_*
-big_anal_process cond_s_o_v_t_*
-big_anal_process cond_v_o_v_t_*
-big_anal_process cond_v_d_v_t_*
-long_anal_process strs_s_o_v_t_*
-long_anal_process strs_v_o_v_t_*
-long_anal_process strs_v_d_v_t_*
-long_anal_process thrs_s_o_v_t_*
-long_anal_process thrs_v_o_v_t_*
-long_anal_process thrs_v_d_v_t_*
-long_anal_process enrg_s_o_v_t_*
-long_anal_process enrg_v_o_v_t_*
-long_anal_process enrg_v_d_v_t_*
-long_anal_process load_s_o_v_t_*
-long_anal_process load_v_o_v_t_*
-long_anal_process load_v_d_v_t_*
diff --git a/data/betas.txt b/data/betas.txt
deleted file mode 100644
index b5dcd99..0000000
--- a/data/betas.txt
+++ /dev/null
@@ -1 +0,0 @@
-64 53.8174 45.2548 38.0546 32 26.9087 22.6274 19.0273 16. 13.4543 11.3137 9.51366 8. 6.72717 5.65685 4.75683 4. 3.36359 2.82843 2.37841 2. 1.68179 1.41421 1.18921 1. 0.840896 0.707107 0.594604 0.5 0.420448 0.353553 0.297302 0.25 0.210224 0.176777 0.148651 0.125 0.105112 0.0883883 0.0743254 0.0625 0.052556 0.0441942 0.0371627 0.03125 0.026278 0.0220971 0.0185814 0.015625 0.013139 0.0110485 0.00929068 0.0078125 0.0065695 0.00552427
diff --git a/data/processed/avln_s_o_v_t.txt b/data/processed/avln_s_o_v_t.txt
deleted file mode 100644
index ef45386..0000000
--- a/data/processed/avln_s_o_v_t.txt
+++ /dev/null
@@ -1,341 +0,0 @@
-128 0.000172633 0.00465921 5.6642e-05 0.022924 0.000760558 0.270229 0.013557 4.13313 0.274498
-128 0.000205297 0.00425119 4.54963e-05 0.0147892 0.000469807 0.129437 0.00682385 1.57699 0.114229
-128 0.000244141 0.00399484 3.61544e-05 0.00934275 0.000265107 0.0543959 0.00307522 0.502337 0.0418035
-128 0.000290334 0.00389487 2.94825e-05 0.00621284 0.000132047 0.0204319 0.00111515 0.124628 0.0111155
-128 0.000345267 0.00398488 2.60485e-05 0.00485145 5.9408e-05 0.00832753 0.000323 0.0252346 0.00235361
-128 0.000410594 0.00428158 2.56968e-05 0.00471772 3.63736e-05 0.00588476 0.000101524 0.00945251 0.000452051
-128 0.000488281 0.00482581 2.69522e-05 0.00518659 3.34452e-05 0.00601069 6.09775e-05 0.00798662 0.000160527
-128 0.000580668 0.00562401 2.92913e-05 0.0061195 3.78559e-05 0.00727786 8.07566e-05 0.0102213 0.000296702
-128 0.000690534 0.00650249 3.18599e-05 0.00722848 4.47097e-05 0.0090554 0.000117232 0.0142351 0.000521274
-128 0.000821188 0.00765217 3.48961e-05 0.00867117 5.3401e-05 0.0114069 0.000200927 0.0203059 0.00154612
-128 0.000976563 0.00899248 3.82252e-05 0.0103836 5.97658e-05 0.0140643 0.000195772 0.0253837 0.00118414
-128 0.00116134 0.010509 4.18492e-05 0.012417 7.071e-05 0.0177733 0.000248773 0.0354491 0.00137187
-128 0.00138107 0.0123508 4.6136e-05 0.0150597 8.45945e-05 0.0230081 0.000320817 0.0506315 0.00180964
-128 0.00164238 0.014361 5.05939e-05 0.0180638 0.000102891 0.0297528 0.000453924 0.0747081 0.00287916
-128 0.00195313 0.0167896 5.57942e-05 0.0219176 0.000123882 0.0388145 0.000623928 0.108052 0.00481425
-128 0.00232267 0.0196389 6.16288e-05 0.0266389 0.000149559 0.0510619 0.000776795 0.156882 0.00562319
-128 0.00276214 0.0228907 4.83572e-05 0.0326892 0.000134546 0.0700355 0.000840648 0.25306 0.00750016
-128 0.00328475 0.0267014 5.37932e-05 0.0402728 0.000173526 0.0974643 0.00128877 0.419069 0.0133345
-128 0.00390625 0.0311438 6.00726e-05 0.0499525 0.000221705 0.136759 0.00185642 0.680387 0.021343
-128 0.00464534 0.0360582 5.47155e-05 0.0617968 0.000239448 0.19557 0.00247915 1.1835 0.0357306
-128 0.00552427 0.0418226 0.000106408 0.0773559 0.000537822 0.283003 0.00606549 1.97616 0.0908362
-128 0.0065695 0.0486858 0.000120126 0.0977828 0.000706557 0.415412 0.00914686 3.38282 0.157342
-128 0.0078125 0.0564543 0.000135674 0.123659 0.000950857 0.620193 0.0145504 6.07379 0.293139
-128 0.00929068 0.0653805 0.000154854 0.159307 0.00134177 0.980247 0.02551 11.9605 0.647998
-128 0.0110485 0.0757212 0.000125075 0.205341 0.00130096 1.51516 0.0296323 22.2159 0.896933
-128 0.013139 0.0869128 0.000142846 0.264153 0.00178662 2.36216 0.0466771 41.3217 1.60056
-128 0.015625 0.100008 0.000164105 0.343295 0.0024227 3.66605 0.0719884 74.8208 2.73706
-128 0.0185814 0.115295 0.000191322 0.458108 0.00365041 6.29842 0.140352 166.772 6.91132
-128 0.0220971 0.131594 0.000220858 0.597927 0.00528851 10.2184 0.271036 342.837 19.0703
-128 0.026278 0.150579 0.000258521 0.800323 0.00773262 17.3035 0.475104 716.022 39.6613
-128 0.03125 0.171271 0.000299975 1.04978 0.010759 27.4102 0.781777 1350.43 76.5192
-128 0.0371627 0.194378 0.000351451 1.39954 0.0157325 46.1769 1.32606 2804.47 137.354
-128 0.0441942 0.219164 0.000408145 1.82573 0.0223796 73.7229 2.40306 5489.23 343.181
-128 0.052556 0.245652 0.000475835 2.39145 0.0318127 118.863 3.99652 10689.3 631.811
-128 0.0625 0.273117 0.000539785 2.95446 0.0423871 170.98 6.52385 18218.1 1315.43
-128 0.0743254 0.301923 0.000619231 3.71376 0.0601061 263.756 11.5857 34990.2 2964.14
-128 0.0883883 0.331293 0.000687078 4.34686 0.0691474 324.757 12.7469 44026.5 2823.42
-128 0.105112 0.362211 0.000770993 5.17479 0.088267 436.003 19.2782 67824.9 5327.53
-128 0.125 0.393867 0.000857091 6.01571 0.103223 534.125 24.6444 87254.8 7923.36
-128 0.148651 0.421518 0.000917582 6.45199 0.115826 583.927 30.8998 102805 10849
-128 0.176777 0.451056 0.00100934 7.25288 0.124762 665.734 28.946 110816 8381.94
-128 0.210224 0.479871 0.00108887 7.79026 0.13131 698.344 29.958 113291 8620.22
-128 0.25 0.505494 0.00117386 8.29522 0.149625 773.067 37.6205 134773 12023.8
-128 0.297302 0.530103 0.0012478 8.53443 0.152622 760.621 37.1222 127678 11643.8
-128 0.353553 0.549982 0.0013362 8.83345 0.164294 785.358 41.5382 133546 13667.4
-128 0.420448 0.567628 0.00114429 8.67974 0.132037 717.497 31.6104 115565 9898.05
-128 0.594604 0.586899 0.0012709 8.34968 0.131351 617.019 28.4417 89188.7 8030.64
-128 0.5 0.580809 0.00122071 8.76968 0.130701 686.719 27.2591 100536 7070
-128 0.707107 0.586767 0.00129519 7.53164 0.107861 455.986 17.7281 52234.3 3642.44
-128 0.840896 0.586525 0.00136909 7.23594 0.113831 427.455 19.7908 50021.5 4347
-128 1.18921 0.545754 0.00138543 5.2717 0.0781657 213.346 9.0894 16780.8 1349.98
-128 1.41421 0.51559 0.00138886 4.37246 0.066983 148.773 7.20715 10170.4 1059.99
-128 1.68179 0.476522 0.00136111 3.40875 0.0498646 88.7132 4.01636 4575.03 453.455
-128 11.3137 0.0577039 0.00123911 0.0689686 0.00186712 0.0948374 0.00396856 0.156593 0.0102444
-128 13.4543 0.0397666 0.0012509 0.0434407 0.00155097 0.051005 0.00249713 0.0667819 0.00507543
-128 16 0.0210815 0.00116089 0.0226298 0.00142428 0.0260838 0.0024554 0.0340638 0.00578974
-128 19.0273 0.00867571 0.000971958 0.00947347 0.00119249 0.011069 0.00182519 0.0142601 0.00331187
-128 1 0.570843 0.00138872 6.31007 0.0935877 307.643 12.7746 28657.8 2249.99
-128 2.37841 0.38279 0.00127533 1.87559 0.0267059 27.4916 1.34671 822.441 94.1497
-128 2.82843 0.334228 0.00123274 1.34274 0.0182353 14.2 0.620614 293.814 29.5025
-128 22.6274 0.00292291 0.000730727 0.00292291 0.000730727 0.00292291 0.000730727 0.00292291 0.000730727
-128 26.9087 0.000817327 0.000577938 0.000817327 0.000577938 0.000817327 0.000577938 0.000817327 0.000577938
-128 2 0.431611 0.00132776 2.58624 0.0360515 50.9251 1.96333 1906.68 133.245
-128 3.36359 0.283664 0.00117549 0.91592 0.0108666 6.38104 0.212959 78.272 5.89683
-128 32 0 -nan 0 -nan 0 -nan 0 -nan
-128 38.0546 0 -nan 0 -nan 0 -nan 0 -nan
-128 4.75683 0.19876 0.00114941 0.456821 0.00573956 1.81291 0.0544546 11.3908 0.691786
-128 45.2548 0 -nan 0 -nan 0 -nan 0 -nan
-128 4 0.241328 0.00116738 0.660091 0.00802767 3.50221 0.109281 31.2147 1.97254
-128 5.65685 0.162544 0.00115219 0.319309 0.00421052 0.964237 0.0269221 4.26416 0.228355
-128 53.8174 -nan -nan -nan -nan -nan -nan -nan -nan
-128 6.72717 0.1316 0.00117327 0.226975 0.00342356 0.559023 0.0167471 1.93259 0.1078
-128 64 -nan -nan -nan -nan -nan -nan -nan -nan
-128 8 0.103999 0.00120366 0.158047 0.00286883 0.321419 0.011809 0.897816 0.0686407
-128 9.51366 0.0795434 0.00123019 0.106715 0.00228214 0.175778 0.00643568 0.367255 0.0234396
-16 0.000172633 0.00109647 4.72164e-06 0.00112766 5.31909e-06 0.00120524 1.08756e-05 0.00143109 5.42909e-05
-16 0.000205297 0.0010675 4.63576e-06 0.00108722 5.12659e-06 0.00114079 1.25238e-05 0.00132964 8.37975e-05
-16 0.000244141 0.00106852 4.6267e-06 0.00108276 5.03404e-06 0.00112368 1.22471e-05 0.0012818 8.3447e-05
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-16 0.125 0.220039 0.000109995 0.555955 0.000566528 2.35229 0.00505908 14.748 0.0604726
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-16 0.210224 0.298064 0.000157789 0.958875 0.0011235 5.5797 0.0137638 48.6132 0.22114
-16 0.25 0.322059 0.000175537 1.10305 0.00135739 6.96207 0.0180652 65.9585 0.315679
-16 0.297302 0.343604 0.000193609 1.23702 0.00159985 8.33081 0.0227455 84.4664 0.422299
-16 0.353553 0.361742 0.000211079 1.34461 0.00181738 9.42399 0.0269499 99.6784 0.518448
-16 0.420448 0.375877 0.000227596 1.41767 0.00199131 10.0872 0.0301669 108.523 0.594709
-16 0.594604 0.391932 0.000257376 1.45352 0.00215471 9.93707 0.0312154 101.874 0.595822
-16 0.5 0.385333 0.000242415 1.44652 0.00209231 10.1576 0.0315217 107.76 0.629795
-16 0.707107 0.394741 0.000271961 1.43434 0.00218557 9.45081 0.030235 92.6343 0.556253
-16 0.840896 0.394173 0.000286601 1.39452 0.00219585 8.79112 0.0287443 81.8606 0.498425
-16 1.18921 0.378585 0.000313382 1.24143 0.00212909 6.98754 0.0245482 57.3011 0.37809
-16 1.41421 0.363031 0.000323905 1.1272 0.00202778 5.87184 0.0213281 44.178 0.297078
-16 1.68179 0.341821 0.000331709 0.995106 0.00188794 4.73857 0.017825 32.2353 0.220842
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diff --git a/data/processed/avln_v_d_v_t.txt b/data/processed/avln_v_d_v_t.txt
deleted file mode 100644
index 190dec8..0000000
--- a/data/processed/avln_v_d_v_t.txt
+++ /dev/null
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diff --git a/data/processed/avln_v_o_v_t.txt b/data/processed/avln_v_o_v_t.txt
deleted file mode 100644
index 6853a23..0000000
--- a/data/processed/avln_v_o_v_t.txt
+++ /dev/null
@@ -1,322 +0,0 @@
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-32 0.105112 0.285486 0.000246789 1.11181 0.00269017 9.50735 0.0540235 132.111 1.42633
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-32 0.840896 0.565272 0.00083559 3.59035 0.0152909 52.1688 0.504149 1202.31 22.0663
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-32 1.41421 0.502013 0.000940762 2.55835 0.0121215 26.6476 0.272439 424.728 8.01358
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-32 13.4543 0.0228372 0.000781808 0.0295747 0.00138315 0.0463977 0.003888 0.0925681 0.0150334
-32 16 0.018496 0.000829733 0.0248643 0.00162728 0.0422527 0.00522705 0.0956363 0.0215177
-32 19.0273 0.0151705 0.000837257 0.019546 0.00142963 0.0300183 0.00360162 0.0569881 0.0115162
-32 1 0.552063 0.000875994 3.30603 0.0143246 43.3597 0.411191 884.029 15.2525
-32 2.37841 0.382268 0.000993957 1.38439 0.0078277 8.97799 0.104736 85.8598 1.82074
-32 2.82843 0.333415 0.000996903 1.05441 0.00650374 5.69601 0.0723236 44.8777 1.07213
-32 22.6274 0.012517 0.00076282 0.0166428 0.00142625 0.0274116 0.00407984 0.0581798 0.0142687
-32 26.9087 0.0114843 0.000773372 0.0145303 0.00126269 0.0216103 0.00283184 0.0387338 0.00746176
-32 2 0.427706 0.000982568 1.75603 0.00927932 13.5528 0.149681 156.617 3.0946
-32 3.36359 0.286728 0.00100672 0.798163 0.00565479 3.68916 0.0566088 25.1832 0.781123
-32 32 0.00995463 0.000762204 0.0125475 0.00137584 0.0196777 0.00395348 0.0408834 0.0137913
-32 38.0546 0.00860183 0.000758967 0.0115851 0.0012822 0.0181484 0.00277418 0.0330648 0.00692273
-32 4.75683 0.191218 0.0009957 0.407755 0.00381171 1.31063 0.025018 5.97562 0.228387
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-32 4 0.236923 0.000996526 0.569472 0.00447357 2.1396 0.0336686 11.4764 0.330729
-32 5.65685 0.146326 0.000973703 0.27637 0.00311611 0.752542 0.0160053 2.8305 0.103537
-32 53.8174 0.00793651 0.000667248 0.00976099 0.00100967 0.0136836 0.00201624 0.0223499 0.0047947
-32 6.72717 0.104628 0.000930344 0.174865 0.00245829 0.398317 0.0102777 1.22091 0.0547985
-32 64 0.00807574 0.000630265 0.00998528 0.0010119 0.0145204 0.00228911 0.025739 0.00612268
-32 8 0.0736944 0.000900252 0.113285 0.00209637 0.229339 0.00763606 0.614301 0.0357511
-32 9.51366 0.0488457 0.000840579 0.0690146 0.00172756 0.123972 0.00559489 0.291508 0.0234495
-64 0.000172633 0.00474104 4.3085e-05 0.0124726 0.000238261 0.0586027 0.00198236 0.381424 0.0206889
-64 0.000205297 0.00401737 3.53484e-05 0.0084052 0.000156576 0.0309384 0.00105885 0.164915 0.00836823
-64 0.000244141 0.00346512 2.87139e-05 0.00554564 9.42347e-05 0.0145433 0.000529989 0.0597297 0.00353298
-64 0.000290334 0.00307222 2.39874e-05 0.00387447 5.0801e-05 0.00661953 0.000210643 0.0173776 0.00113146
-64 0.000345267 0.00293509 2.18423e-05 0.00321141 3.1029e-05 0.00399045 8.88102e-05 0.0064809 0.000397287
-64 0.000410594 0.00309634 2.18511e-05 0.00321486 2.48548e-05 0.00348844 4.03925e-05 0.00415945 0.000107421
-64 0.000488281 0.00345558 2.29945e-05 0.00355753 2.51579e-05 0.00377572 3.4766e-05 0.00425846 7.34061e-05
-64 0.000580668 0.00401534 2.48753e-05 0.00416021 2.74236e-05 0.00445441 3.63999e-05 0.00505621 6.30471e-05
-64 0.000690534 0.00465112 2.68754e-05 0.00484979 3.03015e-05 0.0052677 4.34215e-05 0.00616515 8.60657e-05
-64 0.000821188 0.00552431 2.94144e-05 0.00580568 3.41911e-05 0.00642206 5.62127e-05 0.00784438 0.000154673
-64 0.000976563 0.00650165 3.20457e-05 0.00688357 3.77298e-05 0.00770737 6.00907e-05 0.00954206 0.000136623
-64 0.00116134 0.00763424 3.49836e-05 0.00819236 4.29865e-05 0.00943946 7.68272e-05 0.0123693 0.000203832
-64 0.00138107 0.00901043 3.82928e-05 0.00979294 4.9011e-05 0.0115996 9.63995e-05 0.0160423 0.000283821
-64 0.00164238 0.0106332 4.18972e-05 0.0117051 5.50749e-05 0.0141721 0.000111951 0.0202262 0.000340395
-64 0.00195313 0.0124838 4.58892e-05 0.0140184 6.36976e-05 0.017669 0.000141606 0.0270099 0.000459298
-64 0.00232267 0.0145811 5.01951e-05 0.0167163 7.38141e-05 0.0219732 0.000183713 0.0361489 0.000684424
-64 0.00276214 0.0172212 5.52741e-05 0.0202062 8.59852e-05 0.0277621 0.000230148 0.0488977 0.000893088
-64 0.00328475 0.0199822 6.03352e-05 0.0239887 9.93725e-05 0.0344639 0.000287832 0.0650728 0.00118943
-64 0.00390625 0.0235687 6.68808e-05 0.0293515 0.000122496 0.0455521 0.000441422 0.0984635 0.0024879
-64 0.00464534 0.0276515 7.39241e-05 0.0356719 0.000148301 0.0594245 0.0006189 0.143562 0.00419277
-64 0.00552427 0.0323366 8.18626e-05 0.0434823 0.000176357 0.0776969 0.000725726 0.201803 0.00418554
-64 0.0065695 0.0377726 6.42601e-05 0.0532601 0.000156237 0.104743 0.000780646 0.314838 0.0057693
-64 0.0078125 0.0440807 7.16369e-05 0.0656435 0.000196057 0.143182 0.00109709 0.491681 0.00874408
-64 0.00929068 0.0514423 8.01219e-05 0.0813757 0.000250714 0.199298 0.00163087 0.796802 0.0147815
-64 0.0110485 0.0597997 8.96223e-05 0.100839 0.000314915 0.27548 0.00228724 1.24504 0.0232229
-64 0.013139 0.0695684 0.000100912 0.12627 0.000412855 0.394924 0.00362375 2.11354 0.0458565
-64 0.015625 0.0808621 0.000114259 0.159592 0.00054323 0.57682 0.0053769 3.60743 0.0735084
-64 0.0185814 0.0935722 0.000129399 0.201504 0.000710811 0.838236 0.00817238 6.08033 0.13503
-64 0.0220971 0.108516 0.000147885 0.258199 0.000959616 1.26521 0.0126029 10.8717 0.222541
-64 0.026278 0.125344 0.000169926 0.333709 0.00134792 1.9795 0.0217122 20.998 0.464501
-64 0.03125 0.144487 0.000195319 0.430408 0.00182144 3.01146 0.0337408 37.4299 0.818512
-64 0.0371627 0.166009 0.000224935 0.555541 0.00249668 4.60628 0.0581327 68.443 2.00439
-64 0.0441942 0.19083 0.000261759 0.728982 0.00344438 7.27583 0.0854639 126.222 2.7289
-64 0.052556 0.217451 0.000304613 0.953222 0.0049411 11.6609 0.154884 250.809 6.382
-64 0.0625 0.247878 0.000355729 1.24892 0.00698595 18.6039 0.255786 481.667 11.8699
-64 0.0743254 0.280348 0.000416597 1.63642 0.00995415 29.8135 0.435172 934.267 23.9703
-64 0.0883883 0.315663 0.000484561 2.10361 0.0137765 45.6765 0.711997 1700.38 46.2475
-64 0.105112 0.352726 0.000561702 2.6703 0.0188525 68.5068 1.15196 3008.07 88.6478
-64 0.125 0.390785 0.000651177 3.36664 0.0262598 103.488 1.93651 5474.94 181.885
-64 0.148651 0.429471 0.000605164 4.0693 0.0272827 140.446 2.22317 8270.81 233.234
-64 0.176777 0.466555 0.000683102 4.79191 0.0345729 184.293 3.21302 12274.7 375.696
-64 0.210224 0.50356 0.000762944 5.49022 0.0407335 223.361 3.97885 15649.7 491.268
-64 0.25 0.537138 0.000839705 6.05298 0.0462697 253.268 4.72716 18378.4 609.298
-64 0.297302 0.566904 0.000917349 6.51592 0.050557 272.769 5.1994 19791.1 681.008
-64 0.353553 0.594402 0.00099735 6.88359 0.0549934 285.465 6.22141 20928.7 1068.9
-64 0.420448 0.616219 0.0010803 7.14378 0.0576026 289.038 6.05113 20310.7 941.178
-64 0.594604 0.640223 0.00123686 7.0937 0.0587579 258.423 5.10937 16009 555.771
-64 0.5 0.632482 0.00116577 7.2805 0.0586512 282.496 5.27625 18428.6 590.067
-64 0.707107 0.641179 0.00131674 6.86217 0.0590445 235.83 4.9556 13798.1 550.116
-64 0.840896 0.635141 0.00139129 6.4519 0.0553503 198.772 4.01613 10211.5 373.744
-64 1.18921 0.592451 0.00148973 5.02178 0.0447841 117.547 2.41792 4538.28 163.21
-64 1.41421 0.558605 0.00153411 4.27919 0.038919 85.432 1.7451 2754.06 99.2275
-64 1.68179 0.521529 0.00158072 3.57231 0.0353909 62.2082 1.49547 1790.71 86.0932
-64 11.3137 0.085387 0.00234098 0.151659 0.00687525 0.381766 0.031345 1.30812 0.174672
-64 13.4543 0.0642891 0.00238539 0.10913 0.00692604 0.265759 0.0330906 0.920017 0.190847
-64 16 0.0514668 0.00236895 0.0770911 0.00523677 0.149742 0.0171464 0.37672 0.0676516
-64 19.0273 0.0482824 0.00269551 0.076145 0.006328 0.157061 0.0218172 0.419656 0.0888829
-64 1 0.614906 0.00143551 5.71266 0.0506166 155.47 3.30016 7102.54 276.669
-64 2.37841 0.430553 0.00162921 2.22112 0.0239862 25.7072 0.654872 481.437 23.6617
-64 2.82843 0.379092 0.00164225 1.66258 0.0192474 15.3847 0.420154 228.375 12.2325
-64 22.6274 0.0420827 0.00264753 0.0589634 0.00475511 0.0977175 0.0109832 0.190204 0.0288655
-64 26.9087 0.0393812 0.00278467 0.0551336 0.00496067 0.0908579 0.0112974 0.174965 0.0293289
-64 2 0.47462 0.00160464 2.85194 0.0293473 41.092 0.952121 953.945 38.8588
-64 3.36359 0.333943 0.00169789 1.27059 0.016289 9.68582 0.284161 116.942 6.48905
-64 32 0.0322222 0.0027721 0.0484127 0.00551002 0.0884127 0.0139149 0.19127 0.0387266
-64 38.0546 0.0355172 0.00309385 0.0555172 0.00780637 0.120345 0.029604 0.353448 0.12969
-64 4.75683 0.242015 0.0017763 0.674556 0.0104256 3.25102 0.102828 23.2371 1.2647
-64 45.2548 0.0329871 0.00295558 0.0479315 0.00588582 0.0865683 0.0152948 0.190086 0.0434972
-64 4 0.284519 0.00171761 0.915045 0.0126245 5.44007 0.162328 49.4337 2.70018
-64 5.65685 0.202586 0.00186132 0.496487 0.00930633 2.03616 0.0794125 12.4115 0.864757
-64 53.8174 0.033728 0.00267297 0.0518998 0.00607757 0.103937 0.019872 0.268309 0.0741898
-64 6.72717 0.165366 0.00193431 0.35326 0.00793003 1.18806 0.0591541 5.93733 0.601287
-64 64 0.0328871 0.00257859 0.0456927 0.00448517 0.0739232 0.00984158 0.138242 0.0246909
-64 8 0.134458 0.00206041 0.265785 0.00732934 0.789592 0.044267 3.3632 0.344517
-64 9.51366 0.103874 0.00212805 0.188425 0.00651011 0.491348 0.0309917 1.76341 0.176441
diff --git a/data/processed/cond_s_o_v_t.txt b/data/processed/cond_s_o_v_t.txt
deleted file mode 100644
index d8657f6..0000000
--- a/data/processed/cond_s_o_v_t.txt
+++ /dev/null
@@ -1,341 +0,0 @@
-128 0.000172633 0.0089842 0.000109835 1.20638e-05 9.14684e-07 8.5082e-08 1.17821e-08 8.36646e-10 1.76413e-10
-128 0.000205297 0.00914547 0.000124032 1.53839e-05 1.4114e-06 1.41496e-07 2.76915e-08 1.99205e-09 6.56342e-10
-128 0.000244141 0.00914072 0.000118088 1.39449e-05 1.29697e-06 1.2295e-07 2.47671e-08 1.68212e-09 5.60187e-10
-128 0.000290334 0.00898619 0.000107932 1.16493e-05 8.47861e-07 7.84166e-08 1.00774e-08 7.18868e-10 1.39114e-10
-128 0.000345267 0.00890508 0.000111055 1.23331e-05 9.13143e-07 8.72184e-08 1.12124e-08 8.33829e-10 1.60002e-10
-128 0.000410594 0.00909314 0.000118155 1.39607e-05 1.36555e-06 1.25472e-07 2.96005e-08 1.86473e-09 7.56609e-10
-128 0.000488281 0.00911762 0.000110436 1.2196e-05 9.18292e-07 8.59328e-08 1.17474e-08 8.4326e-10 1.73562e-10
-128 0.000580668 0.00926606 0.00011776 1.38673e-05 1.23127e-06 1.17418e-07 2.23656e-08 1.51602e-09 4.92065e-10
-128 0.000690534 0.00934762 0.000126868 1.60955e-05 1.26892e-06 1.37083e-07 1.89327e-08 1.61015e-09 3.23306e-10
-128 0.000821188 0.00911254 0.000112686 1.26981e-05 8.82086e-07 8.58864e-08 1.06033e-08 7.78076e-10 1.58702e-10
-128 0.000976563 0.00904161 0.000107693 1.15978e-05 7.90051e-07 7.39697e-08 8.45543e-09 6.2418e-10 1.04029e-10
-128 0.00116134 0.00946419 0.000127953 1.63719e-05 1.46897e-06 1.51153e-07 3.05633e-08 2.15788e-09 7.92006e-10
-128 0.00138107 0.00933179 0.000121896 1.48587e-05 1.23576e-06 1.23566e-07 2.14513e-08 1.5271e-09 4.5138e-10
-128 0.00164238 0.0094902 0.000135382 1.83283e-05 1.71255e-06 1.87284e-07 3.65479e-08 2.93281e-09 9.05725e-10
-128 0.00195313 0.00945418 0.000131578 1.73127e-05 1.75597e-06 1.84291e-07 3.98655e-08 3.08344e-09 1.04936e-09
-128 0.00232267 0.00967393 0.000137978 1.9038e-05 1.74887e-06 1.93857e-07 4.00276e-08 3.05855e-09 1.13477e-09
-128 0.00276214 0.00958268 9.35836e-05 1.75158e-05 1.14889e-06 1.75981e-07 2.31397e-08 2.63988e-09 5.51802e-10
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-64 0.00929068 0.0204676 0.000106815 9.12754e-05 3.12687e-06 2.1021e-06 1.94384e-07 7.82187e-08 1.74607e-08
-64 0.0110485 0.0210954 0.000114396 0.000104691 3.7688e-06 2.75209e-06 2.22381e-07 1.13631e-07 1.64161e-08
-64 0.013139 0.0219267 0.000121865 0.000118809 3.91635e-06 3.10276e-06 2.14091e-07 1.22702e-07 1.44422e-08
-64 0.015625 0.0226234 0.000127341 0.000129725 3.8789e-06 3.30154e-06 1.92787e-07 1.20367e-07 1.23545e-08
-64 0.0185814 0.0237492 0.000140493 0.000157906 5.01748e-06 4.61971e-06 3.08915e-07 2.01401e-07 2.4354e-08
-64 0.0220971 0.0248999 0.000148289 0.000175917 5.26257e-06 5.18708e-06 3.07134e-07 2.21557e-07 2.27838e-08
-64 0.026278 0.0267047 0.000164854 0.000217415 6.63508e-06 7.21308e-06 4.4467e-07 3.52194e-07 3.6643e-08
-64 0.03125 0.0295571 0.000186467 0.000278158 7.74633e-06 9.74537e-06 5.03615e-07 4.80045e-07 4.00759e-08
-64 0.0371627 0.0319359 0.000206899 0.000342459 9.2992e-06 1.30032e-05 6.59799e-07 6.91802e-07 5.75239e-08
-64 0.0441942 0.0355426 0.000191049 0.000437995 9.42984e-06 1.83237e-05 7.31487e-07 1.06706e-06 6.92977e-08
-64 0.052556 0.0405388 0.000215465 0.000557104 1.13564e-05 2.49345e-05 9.48515e-07 1.54761e-06 9.65839e-08
-64 0.0625 0.0470976 0.000247362 0.000734256 1.40264e-05 3.59603e-05 1.21032e-06 2.36089e-06 1.27105e-07
-64 0.0743254 0.0561459 0.000289567 0.00100619 1.80663e-05 5.47135e-05 1.71282e-06 3.91668e-06 1.98668e-07
-64 0.0883883 0.0656052 0.000323521 0.00125599 2.09473e-05 7.23697e-05 1.97475e-06 5.26546e-06 2.31468e-07
-64 0.105112 0.0807829 0.000370865 0.00165049 2.62238e-05 0.000105425 2.62266e-06 8.25227e-06 3.26009e-07
-64 0.125 0.0994504 0.000418126 0.00209796 3.25364e-05 0.000149273 3.46337e-06 1.27034e-05 4.61991e-07
-64 0.148651 0.123505 0.000462603 0.00256802 3.86515e-05 0.000199065 4.11994e-06 1.79273e-05 5.20521e-07
-64 0.176777 0.15161 0.000509369 0.00311348 4.74655e-05 0.000268823 5.68114e-06 2.70357e-05 8.25079e-07
-64 0.210224 0.186907 0.000540816 0.00350978 5.34576e-05 0.000322019 6.67931e-06 3.42925e-05 9.79333e-07
-64 0.25 0.22458 0.000565139 0.00383259 5.78156e-05 0.000365069 7.34298e-06 4.01117e-05 1.06563e-06
-64 0.297302 0.267472 0.000581361 0.00405577 6.204e-05 0.000402369 8.30418e-06 4.61876e-05 1.29864e-06
-64 0.353553 0.315653 0.000589536 0.00417063 6.34758e-05 0.000417216 8.53783e-06 4.83501e-05 1.31447e-06
-64 0.420448 0.367269 0.000594472 0.00424077 6.50307e-05 0.000430743 8.91938e-06 5.07478e-05 1.41594e-06
-64 0.594604 0.4812 0.000563671 0.00381269 5.88995e-05 0.000368735 7.86159e-06 4.16297e-05 1.24513e-06
-64 0.5 0.423647 0.000586216 0.0041238 6.31985e-05 0.000413223 8.5083e-06 4.79287e-05 1.31862e-06
-64 0.707107 0.540335 0.000544123 0.00355284 5.44798e-05 0.000329981 6.83751e-06 3.56165e-05 9.81091e-07
-64 0.840896 0.602137 0.000508714 0.00310548 4.78855e-05 0.000270447 5.77643e-06 2.75163e-05 8.32386e-07
-64 1.18921 0.719084 0.00041209 0.00203782 3.15369e-05 0.000144173 3.07523e-06 1.19349e-05 3.48481e-07
-64 1.41421 0.772358 0.000355339 0.00151519 2.3996e-05 9.40082e-05 2.12292e-06 6.90968e-06 2.25505e-07
-64 1.68179 0.819775 0.000303019 0.00110185 1.72664e-05 5.77621e-05 1.28833e-06 3.57755e-06 1.161e-07
-64 11.3137 0.99713 1.4489e-05 2.51919e-06 4.03376e-08 6.38365e-09 1.5404e-10 1.95255e-11 7.25545e-13
-64 13.4543 0.998416 1.00526e-05 1.21266e-06 2.00884e-08 2.1686e-09 5.93142e-11 4.84251e-12 2.29059e-13
-64 16 0.999207 6.82228e-06 5.58521e-07 1.00892e-08 7.13596e-10 2.38973e-11 1.22151e-12 7.36501e-14
-64 19.0273 0.999668 4.19686e-06 2.11364e-07 4.36814e-09 1.86465e-10 6.88794e-12 2.28967e-13 1.27822e-14
-64 1 0.661609 0.000462798 0.00257018 3.98511e-05 0.000204656 4.38845e-06 1.90573e-05 5.68618e-07
-64 2.37841 0.895143 0.000200813 0.000483911 7.66292e-06 1.69492e-05 3.87276e-07 7.04644e-07 2.38166e-08
-64 2.82843 0.922829 0.000157714 0.000298486 4.74561e-06 8.26282e-06 1.87203e-07 2.7025e-07 9.01877e-09
-64 22.6274 0.999915 1.98253e-06 4.71649e-08 1.46595e-09 2.95337e-11 1.68389e-12 2.5788e-14 2.41329e-15
-64 26.9087 0.999989 6.09776e-07 5.94924e-09 3.69572e-10 3.37681e-12 2.84814e-13 2.18534e-15 2.55071e-16
-64 2 0.860635 0.000247523 0.000735212 1.15819e-05 3.16557e-05 7.08089e-07 1.60968e-06 5.23963e-08
-64 3.36359 0.94446 0.00012443 0.000185793 2.93359e-06 4.0209e-06 9.22987e-08 1.03272e-07 3.65305e-09
-64 32 0.999999 1.25699e-07 2.52804e-10 6.12487e-11 1.23117e-13 2.98603e-14 6.00225e-17 1.45576e-17
-64 38.0546 1 6.40727e-17 6.5685e-29 5.19285e-31 5.32352e-43 4.20862e-45 4.31452e-57 3.41093e-59
-64 4.75683 0.973181 7.06405e-05 5.98809e-05 9.3339e-07 7.29326e-07 1.60303e-08 1.04546e-08 3.32138e-10
-64 45.2548 1 6.40727e-17 6.5685e-29 5.19285e-31 5.32352e-43 4.20862e-45 4.31452e-57 3.41093e-59
-64 4 0.960821 9.34839e-05 0.000104871 1.65291e-06 1.71066e-06 3.76094e-08 3.27852e-08 1.01407e-09
-64 5.65685 0.981859 5.27646e-05 3.34093e-05 5.14488e-07 3.01087e-07 6.45276e-09 3.17637e-09 9.61817e-11
-64 53.8174 1 6.40727e-17 6.5685e-29 5.19285e-31 5.32352e-43 4.20862e-45 4.31452e-57 3.41093e-59
-64 6.72717 0.98799 3.95436e-05 1.87644e-05 3.01474e-07 1.30428e-07 3.16382e-09 1.09064e-09 4.22964e-11
-64 64 1 6.40727e-17 6.5685e-29 5.19285e-31 5.32352e-43 4.20862e-45 4.31452e-57 3.41093e-59
-64 8 0.992309 2.8119e-05 9.48815e-06 1.53269e-07 4.71612e-08 1.14131e-09 2.81898e-10 1.06726e-11
-64 9.51366 0.99524 2.03714e-05 4.97991e-06 7.892e-08 1.76523e-08 4.08927e-10 7.47404e-11 2.55801e-12
diff --git a/data/processed/cond_v_d_v_t.txt b/data/processed/cond_v_d_v_t.txt
deleted file mode 100644
index 4d12464..0000000
--- a/data/processed/cond_v_d_v_t.txt
+++ /dev/null
@@ -1,309 +0,0 @@
-128 0.000976563 0.0114219 0.000146636 2.15021e-05 1.69183e-06 2.07307e-07 3.30566e-08 2.8623e-09 8.25472e-10
-128 0.00116134 0.0114702 0.000156768 2.45761e-05 2.02381e-06 2.68136e-07 3.93556e-08 4.09581e-09 8.75676e-10
-128 0.00138107 0.0117174 0.000161159 2.59722e-05 2.56322e-06 3.34394e-07 6.62479e-08 6.5701e-09 1.96227e-09
-128 0.00164238 0.0118183 0.000168695 2.84581e-05 2.76611e-06 3.77681e-07 7.64867e-08 7.65139e-09 2.48302e-09
-128 0.00195313 0.0120296 0.000176744 3.12383e-05 2.87161e-06 4.20712e-07 7.36079e-08 8.24613e-09 2.21639e-09
-128 0.00232267 0.0120279 0.000162128 2.62855e-05 2.06363e-06 2.82029e-07 4.26997e-08 4.25858e-09 1.10449e-09
-128 0.00276214 0.0124632 0.000175207 3.06975e-05 2.76953e-06 4.00781e-07 6.80955e-08 7.67028e-09 1.89666e-09
-128 0.00328475 0.0130465 0.000201768 4.07102e-05 3.57758e-06 6.08413e-07 9.65392e-08 1.27991e-08 3.05009e-09
-128 0.00390625 0.0132045 0.000203608 4.1456e-05 3.40275e-06 5.79528e-07 8.80874e-08 1.15787e-08 2.65031e-09
-128 0.00464534 0.013374 0.000229552 5.26943e-05 6.31491e-06 1.16753e-06 2.75109e-07 3.98781e-08 1.35975e-08
-128 0.0441942 0.0672846 0.00106406 0.00113223 6.41565e-05 6.16666e-05 5.35042e-06 4.11605e-06 5.32139e-07
-128 0.052556 0.0845721 0.00120763 0.00145838 8.84179e-05 9.37744e-05 1.04506e-05 7.81772e-06 1.67053e-06
-128 0.0625 0.106089 0.00135995 0.00184946 9.88916e-05 0.000124011 9.33164e-06 9.77955e-06 1.04704e-06
-128 0.0743254 0.135475 0.00147834 0.00218548 0.000115298 0.000158273 1.12798e-05 1.32937e-05 1.26834e-06
-128 0.0883883 0.170846 0.00163014 0.00265735 0.000142185 0.000213904 1.58563e-05 2.02166e-05 2.03928e-06
-128 0.105112 0.210787 0.00178141 0.00317343 0.000168697 0.000278335 2.01051e-05 2.84586e-05 2.72878e-06
-128 0.125 0.25862 0.00187706 0.00352335 0.000183821 0.000320052 2.28275e-05 3.37901e-05 3.30474e-06
-128 0.148651 0.316645 0.00196697 0.00386899 0.000203614 0.000373613 2.5782e-05 4.14587e-05 3.65474e-06
-128 0.176777 0.375561 0.00204094 0.00416544 0.000229961 0.000432483 3.30616e-05 5.28821e-05 5.44734e-06
-128 0.210224 0.448145 0.00204761 0.00419269 0.000233528 0.000440405 3.43465e-05 5.45355e-05 5.93111e-06
-128 0.25 0.526738 0.00216341 0.00468036 0.000253452 0.000506862 3.77954e-05 6.42377e-05 6.55385e-06
-128 0.297302 0.609954 0.00149199 0.00445209 0.000165714 0.000459071 2.30312e-05 5.4922e-05 3.65697e-06
-128 0.353553 0.705003 0.00154023 0.00474462 0.000180126 0.000512864 2.69948e-05 6.48906e-05 4.76523e-06
-128 0.420448 0.801367 0.0015201 0.00462139 0.000179369 0.000501592 2.76087e-05 6.43466e-05 5.06643e-06
-128 0.594604 1.01346 0.00138691 0.00384704 0.000150573 0.000385374 2.0879e-05 4.53447e-05 3.39786e-06
-128 0.5 0.906134 0.00145325 0.00422385 0.000162323 0.000435704 2.29763e-05 5.26978e-05 3.70498e-06
-128 0.707107 1.11736 0.00135739 0.00368503 0.000138934 0.000347183 1.87383e-05 3.86052e-05 3.09956e-06
-128 0.840896 1.21999 0.00124823 0.00311617 0.000122775 0.000279872 1.62335e-05 3.01474e-05 2.60256e-06
-128 1.18921 1.4176 0.000878964 0.00231773 7.15393e-05 0.000174563 7.383e-06 1.53536e-05 8.82502e-07
-128 1.41421 1.50088 0.000811865 0.00197738 6.19435e-05 0.000139333 6.09036e-06 1.1511e-05 7.22298e-07
-128 1.68179 1.57537 0.000722264 0.001565 4.93893e-05 9.8715e-05 4.34331e-06 7.31792e-06 4.51975e-07
-128 11.3137 1.87552 0.000256815 0.000197862 6.33826e-06 4.49118e-06 2.01142e-07 1.20521e-07 7.3985e-09
-128 13.4543 1.87813 0.000248386 0.000185086 5.85395e-06 4.01275e-06 1.7881e-07 1.02806e-07 6.43558e-09
-128 16 1.87995 0.00024137 0.000174779 5.58452e-06 3.71879e-06 1.65982e-07 9.35607e-08 5.7036e-09
-128 19.0273 1.88121 0.000245707 0.000181116 5.79557e-06 3.93665e-06 1.75807e-07 1.00766e-07 6.26033e-09
-128 1 1.32343 0.000968487 0.0028139 8.50435e-05 0.000229985 9.23406e-06 2.16972e-05 1.13213e-06
-128 2.37841 1.69516 0.000589475 0.00104244 3.279e-05 5.35097e-05 2.34256e-06 3.22555e-06 1.96916e-07
-128 2.82843 1.74034 0.000512227 0.00078713 2.46115e-05 3.49619e-05 1.49494e-06 1.81718e-06 1.03942e-07
-128 22.6274 1.88182 0.000248554 0.000185338 5.96695e-06 4.08036e-06 1.86614e-07 1.06814e-07 6.84183e-09
-128 26.9087 1.88241 0.000248115 0.000184682 5.92558e-06 4.05297e-06 1.8411e-07 1.05337e-07 6.75278e-09
-128 2 1.64139 0.000646177 0.00125264 3.99211e-05 7.12415e-05 3.17968e-06 4.78107e-06 2.9783e-07
-128 3.36359 1.77651 0.000453826 0.000617875 1.91978e-05 2.42065e-05 1.02427e-06 1.10567e-06 6.25967e-08
-128 32 1.88276 0.000240192 0.000173077 5.51847e-06 3.64871e-06 1.67323e-07 9.13605e-08 6.16992e-09
-128 38.0546 1.88293 0.000246477 0.000182253 5.79241e-06 3.93958e-06 1.77062e-07 1.00656e-07 6.42489e-09
-128 4.75683 1.8282 0.000356153 0.000380535 1.20249e-05 1.18699e-05 5.17616e-07 4.33792e-07 2.59361e-08
-128 45.2548 1.88298 0.000242261 0.000176072 5.61254e-06 3.74424e-06 1.7032e-07 9.45019e-08 6.15134e-09
-128 4 1.80552 0.000406961 0.000496851 1.56642e-05 1.76991e-05 7.62326e-07 7.36099e-07 4.28885e-08
-128 5.65685 1.84434 0.000324274 0.000315462 1.02957e-05 9.1168e-06 4.39971e-07 3.18001e-07 2.25101e-08
-128 53.8174 1.8832 0.000240261 0.000173177 5.52541e-06 3.65787e-06 1.64871e-07 9.15905e-08 5.75434e-09
-128 6.72717 1.85699 0.000304987 0.000279051 8.88242e-06 7.4797e-06 3.33725e-07 2.36692e-07 1.4702e-08
-128 64 1.88316 0.000240516 0.000173544 5.41151e-06 3.61009e-06 1.54435e-07 8.78533e-08 5.09568e-09
-128 8 1.86576 0.000279649 0.000234611 7.64907e-06 5.88595e-06 2.69548e-07 1.75525e-07 1.09101e-08
-128 9.51366 1.87122 0.000267489 0.000214651 6.88422e-06 5.06932e-06 2.33685e-07 1.42178e-07 9.64221e-09
-16 0.000172633 0.0945141 6.56945e-05 0.00138105 6.10151e-06 0.000106377 9.8485e-07 1.19131e-05 2.1146e-07
-16 0.000205297 0.0945577 6.57621e-05 0.00138389 6.25418e-06 0.000108054 1.09496e-06 1.25167e-05 2.73678e-07
-16 0.000244141 0.0945922 6.58855e-05 0.00138909 6.22661e-06 0.000108254 1.05385e-06 1.24066e-05 2.46409e-07
-16 0.000290334 0.0945688 6.58976e-05 0.0013896 6.22545e-06 0.000108386 1.03582e-06 1.2402e-05 2.29496e-07
-16 0.000345267 0.094659 6.59133e-05 0.00139026 6.21894e-06 0.000108372 1.034e-06 1.23761e-05 2.33525e-07
-16 0.000410594 0.0947276 6.6e-05 0.00139392 6.21257e-06 0.000108634 1.02329e-06 1.23507e-05 2.28088e-07
-16 0.000488281 0.0947578 6.61129e-05 0.00139869 6.25526e-06 0.00010934 1.04126e-06 1.25211e-05 2.31829e-07
-16 0.000580668 0.0947613 6.59758e-05 0.0013929 6.26694e-06 0.000108805 1.08813e-06 1.25678e-05 2.70621e-07
-16 0.000690534 0.0949269 6.64205e-05 0.00141174 6.42525e-06 0.000112109 1.12179e-06 1.32108e-05 2.67262e-07
-16 0.000821188 0.0948351 6.61996e-05 0.00140237 6.25705e-06 0.000109573 1.03479e-06 1.25282e-05 2.26085e-07
-16 0.000976563 0.0950406 6.67157e-05 0.00142432 6.41384e-06 0.000112958 1.08692e-06 1.31639e-05 2.45422e-07
-16 0.00116134 0.0949762 6.66385e-05 0.00142102 6.38404e-06 0.000112298 1.08021e-06 1.30419e-05 2.4397e-07
-16 0.00138107 0.0952007 6.7099e-05 0.00144073 6.50933e-06 0.000115341 1.10367e-06 1.35588e-05 2.47251e-07
-16 0.00164238 0.0952749 6.72999e-05 0.00144937 6.60001e-06 0.000116832 1.16245e-06 1.39392e-05 2.81272e-07
-16 0.00195313 0.095455 6.75394e-05 0.0014597 6.65884e-06 0.000118243 1.18158e-06 1.41888e-05 2.91005e-07
-16 0.00232267 0.0955641 6.75457e-05 0.00145998 6.61198e-06 0.000117774 1.14626e-06 1.39899e-05 2.67884e-07
-16 0.00276214 0.0958315 6.83709e-05 0.00149587 6.8903e-06 0.000123742 1.23804e-06 1.51924e-05 2.99402e-07
-16 0.00328475 0.0959432 6.84066e-05 0.00149743 6.83723e-06 0.000123216 1.2024e-06 1.49593e-05 2.809e-07
-16 0.00390625 0.0963126 6.91166e-05 0.00152867 7.08017e-06 0.000128427 1.29163e-06 1.60412e-05 3.15016e-07
-16 0.00464534 0.0968535 7.01221e-05 0.00157347 7.32937e-06 0.000134888 1.35997e-06 1.71903e-05 3.36487e-07
-16 0.00552427 0.097253 6.46529e-05 0.00160512 6.71968e-06 0.000137815 1.1986e-06 1.73392e-05 2.75001e-07
-16 0.0065695 0.0976531 6.53824e-05 0.00164155 7.00028e-06 0.000144005 1.34969e-06 1.88175e-05 3.60816e-07
-16 0.0078125 0.0984032 6.65598e-05 0.0017012 7.24509e-06 0.000152211 1.38369e-06 2.01567e-05 3.5335e-07
-16 0.00929068 0.0993552 6.81977e-05 0.00178596 7.73335e-06 0.000165882 1.5493e-06 2.2965e-05 4.15717e-07
-16 0.0110485 0.100327 6.95056e-05 0.00185512 7.95438e-06 0.000174689 1.5702e-06 2.42965e-05 3.98476e-07
-16 0.013139 0.10147 7.12895e-05 0.00195156 8.40972e-06 0.000189445 1.71953e-06 2.71578e-05 4.64662e-07
-16 0.015625 0.103084 7.37748e-05 0.00209 9.08084e-06 0.000211703 1.93045e-06 3.16653e-05 5.42128e-07
-16 0.0185814 0.105167 7.66235e-05 0.00225453 9.88498e-06 0.00023793 2.31505e-06 3.75217e-05 7.91736e-07
-16 0.0220971 0.107669 8.03274e-05 0.00247776 1.07207e-05 0.00027328 2.40767e-06 4.41343e-05 6.8884e-07
-16 0.026278 0.110683 8.44381e-05 0.00273784 1.19055e-05 0.000318085 2.87565e-06 5.44281e-05 9.01956e-07
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diff --git a/data/processed/cond_v_o_v_t.txt b/data/processed/cond_v_o_v_t.txt
deleted file mode 100644
index a89dcdf..0000000
--- a/data/processed/cond_v_o_v_t.txt
+++ /dev/null
@@ -1,322 +0,0 @@
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diff --git a/data/processed/cstr_s_o_v_t.txt b/data/processed/cstr_s_o_v_t.txt
deleted file mode 100644
index f36faa5..0000000
--- a/data/processed/cstr_s_o_v_t.txt
+++ /dev/null
@@ -1,341 +0,0 @@
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diff --git a/data/processed/cstr_v_d_v_t.txt b/data/processed/cstr_v_d_v_t.txt
deleted file mode 100644
index 93d7e3c..0000000
--- a/data/processed/cstr_v_d_v_t.txt
+++ /dev/null
@@ -1,309 +0,0 @@
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diff --git a/data/processed/cstr_v_o_v_t.txt b/data/processed/cstr_v_o_v_t.txt
deleted file mode 100644
index a18d387..0000000
--- a/data/processed/cstr_v_o_v_t.txt
+++ /dev/null
@@ -1,322 +0,0 @@
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diff --git a/data/processed/damg_s_o_v_t.txt b/data/processed/damg_s_o_v_t.txt
deleted file mode 100644
index a0efd62..0000000
--- a/data/processed/damg_s_o_v_t.txt
+++ /dev/null
@@ -1,341 +0,0 @@
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diff --git a/data/processed/damg_v_d_v_t.txt b/data/processed/damg_v_d_v_t.txt
deleted file mode 100644
index e856e6d..0000000
--- a/data/processed/damg_v_d_v_t.txt
+++ /dev/null
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diff --git a/data/processed/damg_v_o_v_t.txt b/data/processed/damg_v_o_v_t.txt
deleted file mode 100644
index 5d468d4..0000000
--- a/data/processed/damg_v_o_v_t.txt
+++ /dev/null
@@ -1,322 +0,0 @@
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diff --git a/data/processed/enrg_s_o_v_t.txt b/data/processed/enrg_s_o_v_t.txt
deleted file mode 100644
index 3044f25..0000000
--- a/data/processed/enrg_s_o_v_t.txt
+++ /dev/null
@@ -1,341 +0,0 @@
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diff --git a/data/processed/enrg_v_d_v_t.txt b/data/processed/enrg_v_d_v_t.txt
deleted file mode 100644
index e24a11e..0000000
--- a/data/processed/enrg_v_d_v_t.txt
+++ /dev/null
@@ -1,309 +0,0 @@
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diff --git a/data/processed/enrg_v_o_v_t.txt b/data/processed/enrg_v_o_v_t.txt
deleted file mode 100644
index af331c2..0000000
--- a/data/processed/enrg_v_o_v_t.txt
+++ /dev/null
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diff --git a/data/processed/load_s_o_v_t.txt b/data/processed/load_s_o_v_t.txt
deleted file mode 100644
index e904926..0000000
--- a/data/processed/load_s_o_v_t.txt
+++ /dev/null
@@ -1,341 +0,0 @@
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diff --git a/data/processed/load_v_d_v_t.txt b/data/processed/load_v_d_v_t.txt
deleted file mode 100644
index 89fb7d0..0000000
--- a/data/processed/load_v_d_v_t.txt
+++ /dev/null
@@ -1,309 +0,0 @@
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diff --git a/data/processed/load_v_o_v_t.txt b/data/processed/load_v_o_v_t.txt
deleted file mode 100644
index 4bce893..0000000
--- a/data/processed/load_v_o_v_t.txt
+++ /dev/null
@@ -1,322 +0,0 @@
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diff --git a/data/processed/strs_s_o_v_t.txt b/data/processed/strs_s_o_v_t.txt
deleted file mode 100644
index 3348326..0000000
--- a/data/processed/strs_s_o_v_t.txt
+++ /dev/null
@@ -1,341 +0,0 @@
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diff --git a/data/processed/strs_v_d_v_t.txt b/data/processed/strs_v_d_v_t.txt
deleted file mode 100644
index 2483472..0000000
--- a/data/processed/strs_v_d_v_t.txt
+++ /dev/null
@@ -1,309 +0,0 @@
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-64 45.2548 38.2321 0.0221227 3.9153 0.0799944 12.7978 0.407662 51.1928 2.66412
-64 4 27.5745 0.0166284 2.21203 0.044366 5.37555 0.160004 15.7467 0.704804
-64 5.65685 30.8282 0.0182707 2.67055 0.0548943 7.23525 0.234758 24.1071 1.30536
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-64 64 38.4981 0.0183839 4.05562 0.0669806 13.342 0.356311 53.8368 2.68447
-64 8 33.326 0.0196285 3.08221 0.062818 8.94196 0.27627 31.5688 1.48316
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diff --git a/data/processed/strs_v_o_v_t.txt b/data/processed/strs_v_o_v_t.txt
deleted file mode 100644
index f170135..0000000
--- a/data/processed/strs_v_o_v_t.txt
+++ /dev/null
@@ -1,322 +0,0 @@
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diff --git a/data/processed/thrs_s_o_v_t.txt b/data/processed/thrs_s_o_v_t.txt
deleted file mode 100644
index 5fec6bc..0000000
--- a/data/processed/thrs_s_o_v_t.txt
+++ /dev/null
@@ -1,341 +0,0 @@
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-64 32 0.773027 0.000416002 0.00276892 7.36017e-05 0.000450137 1.4965e-05 8.66754e-05 3.10319e-06
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-64 5.65685 0.592141 0.00146756 0.0258448 0.00035373 0.00582828 0.000105272 0.0015015 3.51906e-05
-64 53.8174 0.847913 0.000157761 0.000398215 6.92058e-06 1.48449e-05 5.20151e-07 7.66311e-07 5.3142e-08
-64 6.72717 0.62094 0.0014013 0.0235637 0.000310566 0.00492422 8.35242e-05 0.00115741 2.52616e-05
-64 64 0.870654 0.000135654 0.000294433 5.11943e-06 9.45731e-06 3.27999e-07 4.19337e-07 2.84529e-08
-64 8 0.648905 0.00134418 0.0216819 0.000280155 0.00427144 7.0474e-05 0.000941843 1.99281e-05
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diff --git a/data/processed/thrs_v_d_v_t.txt b/data/processed/thrs_v_d_v_t.txt
deleted file mode 100644
index 15709a0..0000000
--- a/data/processed/thrs_v_d_v_t.txt
+++ /dev/null
@@ -1,309 +0,0 @@
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diff --git a/data/processed/thrs_v_o_v_t.txt b/data/processed/thrs_v_o_v_t.txt
deleted file mode 100644
index d4f1d9f..0000000
--- a/data/processed/thrs_v_o_v_t.txt
+++ /dev/null
@@ -1,322 +0,0 @@
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-32 5.65685 0.690917 0.00060868 0.0237114 0.000143417 0.00528 4.02273e-05 0.00131639 1.27757e-05
-32 53.8174 0.977147 7.08327e-05 0.000481657 4.26371e-06 2.37278e-05 4.43358e-07 1.7452e-06 6.02766e-08
-32 6.72717 0.733789 0.000572154 0.0209511 0.000126877 0.00437054 3.44528e-05 0.00103025 1.09562e-05
-32 64 0.981381 5.39372e-05 0.000325833 2.69545e-06 1.33548e-05 2.27223e-07 8.1373e-07 2.42618e-08
-32 8 0.774882 0.000524267 0.0175908 0.000109591 0.00342146 2.94941e-05 0.000768646 9.71518e-06
-32 9.51366 0.810071 0.000475236 0.0144543 9.24564e-05 0.00259067 2.39206e-05 0.000547084 7.57805e-06
-64 0.000172633 1.83646e-1808 0 0 0 0 0 0 0
-64 0.000205297 6.9783e-1655 0 0 0 0 0 0 0
-64 0.000244141 5.12358e-1464 0 0 0 0 0 0 0
-64 0.000290334 9.11657e-1310 0 0 0 0 0 0 0
-64 0.000345267 3.4362e-1143 0 0 0 0 0 0 0
-64 0.000410594 8.00439e-943 0 0 0 0 0 0 0
-64 0.000488281 1.31204e-806 0 0 0 0 0 0 0
-64 0.000580668 3.77922e-677 0 0 0 0 0 0 0
-64 0.000690534 1.10958e-584 0 0 0 0 0 0 0
-64 0.000821188 6.3721e-484 0 0 0 0 0 0 0
-64 0.000976563 3.1847e-405 0 0 0 0 0 0 0
-64 0.00116134 1.07623e-342 0 0 0 0 0 0 0
-64 0.00138107 1.00944e-291 0 0 0 0 0 0 0
-64 0.00164238 8.15444e-245 0 0 0 0 0 0 0
-64 0.00195313 7.23877e-208 0 0 0 0 0 0 0
-64 0.00232267 7.4901e-174 0 0 0 0 0 0 0
-64 0.00276214 2.62712e-144 2.62169e-144 2.7493e-284 0 0 0 0 0
-64 0.00328475 1.13414e-117 1.13399e-117 5.14378e-231 0 0 0 0 0
-64 0.00390625 5.38993e-105 3.87911e-105 6.01901e-206 0 7.32375e-307 0 0 0
-64 0.00464534 1.64013e-86 1.63581e-86 1.07035e-168 0 7.00086e-251 0 0 0
-64 0.00552427 5.89649e-76 4.52094e-76 8.17556e-148 7.71577e-148 1.37065e-219 0 2.38132e-291 0
-64 0.0065695 1.39467e-64 1.00051e-64 8.00821e-125 7.79953e-125 6.17531e-185 0 4.86662e-245 0
-64 0.0078125 2.53564e-54 1.185e-54 1.12339e-104 7.48184e-105 6.84049e-155 5.10481e-155 4.47823e-205 0
-64 0.00929068 3.75077e-46 1.76943e-46 2.50472e-88 1.61516e-88 2.21974e-130 1.54039e-130 2.087e-172 0
-64 0.0110485 7.94375e-40 2.83116e-40 6.41238e-76 5.69253e-76 1.23012e-111 1.21314e-111 2.59239e-147 2.5876e-147
-64 0.013139 1.88761e-33 7.88902e-34 4.97894e-63 3.85982e-63 2.30051e-92 2.09268e-92 1.19186e-121 1.14982e-121
-64 0.015625 7.99167e-29 2.78043e-29 6.18461e-54 5.47658e-54 1.16773e-78 1.14248e-78 2.39944e-103 2.38834e-103
-64 0.0185814 1.23049e-24 2.7566e-25 6.07906e-46 4.04097e-46 8.3418e-67 6.75164e-67 1.30636e-87 1.16395e-87
-64 0.0220971 5.63232e-21 1.15808e-21 1.07291e-38 8.68442e-39 7.506e-56 7.17564e-56 6.03353e-73 5.95924e-73
-64 0.026278 4.81896e-18 3.2127e-19 8.25713e-34 2.87657e-34 6.17604e-49 3.70315e-49 6.61974e-64 5.15004e-64
-64 0.03125 2.26634e-15 2.25364e-16 4.06311e-28 3.13337e-28 5.15462e-40 4.92493e-40 7.85441e-52 7.77544e-52
-64 0.0371627 3.91599e-13 1.41869e-14 1.61014e-24 5.51394e-25 4.68418e-35 3.3934e-35 2.43228e-45 2.17559e-45
-64 0.0441942 2.90789e-11 6.13653e-13 3.01256e-21 3.28218e-22 1.2261e-30 3.04738e-31 8.61816e-40 3.22892e-40
-64 0.052556 1.23593e-09 2.42834e-11 4.71745e-18 1.1844e-18 1.45706e-25 1.1122e-25 1.12225e-32 1.06823e-32
-64 0.0625 2.7678e-08 3.8254e-10 1.1707e-15 8.5554e-17 1.82835e-22 4.49139e-23 5.85559e-29 2.92228e-29
-64 0.0743254 3.82343e-07 4.64019e-09 1.72251e-13 8.02926e-15 2.32419e-19 2.55972e-20 5.15752e-25 1.06249e-25
-64 0.0883883 3.47338e-06 3.87433e-08 1.20083e-11 5.66625e-13 1.3256e-16 1.6385e-17 2.56851e-21 5.84551e-22
-64 0.105112 2.26123e-05 2.34361e-07 4.39402e-10 1.79484e-11 2.57105e-14 2.92346e-15 2.57716e-18 6.27645e-19
-64 0.125 0.00010827 1.08137e-06 9.35489e-09 3.73804e-10 2.54083e-12 2.51854e-13 1.11783e-15 2.28693e-16
-64 0.148651 0.000398176 3.06356e-06 1.12625e-07 3.39061e-09 1.01663e-10 6.19282e-12 1.37955e-13 1.41498e-14
-64 0.176777 0.00117773 8.72564e-06 9.13641e-07 2.83134e-08 2.41963e-09 1.44639e-10 9.61977e-12 8.57586e-13
-64 0.210224 0.00299434 2.12611e-05 5.4244e-06 1.74551e-07 3.59914e-08 2.27921e-09 3.65617e-10 3.42091e-11
-64 0.25 0.00644002 4.22847e-05 2.1456e-05 7.2128e-07 2.83276e-07 2.19181e-08 6.24294e-09 7.78936e-10
-64 0.297302 0.0122824 7.20814e-05 6.23487e-05 1.68923e-06 1.16018e-06 7.38219e-08 3.42421e-08 4.18759e-09
-64 0.353553 0.0220124 0.000127364 0.000194659 5.4136e-06 6.46534e-06 4.72936e-07 3.51685e-07 5.77007e-08
-64 0.420448 0.0355843 0.000190798 0.000436847 1.13344e-05 2.06016e-05 1.28814e-06 1.54162e-06 1.89071e-07
-64 0.594604 0.0776581 0.000386374 0.00179142 3.74895e-05 0.000147603 5.77987e-06 1.68655e-05 1.08474e-06
-64 0.5 0.0545828 0.000280597 0.000944813 2.13283e-05 5.93767e-05 2.82358e-06 5.45877e-06 4.84988e-07
-64 0.707107 0.108127 0.000509443 0.00311438 6.3547e-05 0.000330852 1.29127e-05 4.84586e-05 3.34488e-06
-64 0.840896 0.142144 0.000653514 0.00512496 0.00010467 0.000698022 2.74708e-05 0.000131471 9.34449e-06
-64 1.18921 0.224136 0.000941406 0.0106349 0.000203533 0.00199652 6.69365e-05 0.000497107 2.6771e-05
-64 1.41421 0.272076 0.00111503 0.0149195 0.000287651 0.00332458 0.000117367 0.000992915 6.11919e-05
-64 1.68179 0.3212 0.00123761 0.01838 0.000334945 0.0043799 0.000133242 0.00134626 6.39662e-05
-64 11.3137 0.839608 0.00101 0.0122412 0.00018686 0.0020645 4.7193e-05 0.000419001 1.45263e-05
-64 13.4543 0.868808 0.00087605 0.00920957 0.0001477 0.00139602 3.50526e-05 0.000261783 1.00734e-05
-64 16 0.891762 0.000761183 0.00695279 0.000118915 0.00096032 2.73659e-05 0.000169689 7.79044e-06
-64 19.0273 0.912077 0.000649118 0.00505624 9.31155e-05 0.000631434 2.00147e-05 0.000104046 5.20465e-06
-64 1 0.180225 0.000793563 0.00755691 0.000144628 0.00119584 4.03622e-05 0.000251006 1.39751e-05
-64 2.37841 0.429631 0.00150011 0.027004 0.000446793 0.00729697 0.000177148 0.00239549 8.06579e-05
-64 2.82843 0.48168 0.00154523 0.0286528 0.000446179 0.00763823 0.000162901 0.00238891 6.71799e-05
-64 22.6274 0.930308 0.000546593 0.00358517 7.07157e-05 0.000399271 1.39085e-05 6.00085e-05 3.32056e-06
-64 26.9087 0.943707 0.000459095 0.00252921 5.32094e-05 0.0002487 9.6671e-06 3.39749e-05 2.12709e-06
-64 2 0.376959 0.00137036 0.0225347 0.000394182 0.00578115 0.000160288 0.00186455 7.73638e-05
-64 3.36359 0.53756 0.00160475 0.0309027 0.000453766 0.00818824 0.000154578 0.00247084 5.79748e-05
-64 32 0.955107 0.000378126 0.00171575 3.90837e-05 0.000148224 6.50968e-06 1.83304e-05 1.33025e-06
-64 38.0546 0.964454 0.000302357 0.00109704 2.45485e-05 7.49725e-05 3.1366e-06 7.23153e-06 4.84543e-07
-64 4.75683 0.641948 0.00152781 0.0280105 0.000387477 0.00674015 0.000114289 0.00180167 3.67582e-05
-64 45.2548 0.971207 0.000248693 0.000742181 1.78364e-05 4.32291e-05 2.53066e-06 3.81764e-06 5.50324e-07
-64 4 0.590349 0.00157556 0.0297888 0.000422223 0.00753747 0.000133104 0.00213926 4.5648e-05
-64 5.65685 0.688125 0.00146455 0.0257388 0.000352947 0.00587986 0.000100362 0.00149486 3.22043e-05
-64 53.8174 0.977092 0.000174307 0.000486124 1.00805e-05 2.33479e-05 9.46647e-07 1.62586e-06 1.08659e-07
-64 6.72717 0.733748 0.00136109 0.0222308 0.000307823 0.00472817 8.57098e-05 0.00113706 2.81451e-05
-64 64 0.981274 0.000145693 0.000339625 7.92758e-06 1.48535e-05 7.95392e-07 1.00554e-06 1.08655e-07
-64 8 0.771799 0.00125431 0.0188796 0.000266584 0.00375094 7.14248e-05 0.000852802 2.26995e-05
-64 9.51366 0.808461 0.00114934 0.0158517 0.000230987 0.0029357 6.16839e-05 0.000640262 1.99952e-05
diff --git a/data/ps.txt b/data/ps.txt
deleted file mode 100644
index 1cb301b..0000000
--- a/data/ps.txt
+++ /dev/null
@@ -1 +0,0 @@
-0. 0.01 0.02 0.03 0.04 0.05 0.06 0.07 0.08 0.09 0.1 0.11 0.12 0.13 0.14 0.15 0.16 0.17 0.18 0.19 0.2 0.21 0.22 0.23 0.24 0.25 0.26 0.27 0.28 0.29 0.3 0.31 0.32 0.33 0.34 0.35 0.36 0.37 0.38 0.39 0.4 0.41 0.42 0.43 0.44 0.45 0.46 0.47 0.48 0.49 0.5 0.51 0.52 0.53 0.54 0.55 0.56 0.57 0.58 0.59 0.6 0.61 0.62 0.63 0.64 0.65 0.66 0.67 0.68 0.69 0.7 0.71 0.72 0.73 0.74 0.75 0.76 0.77 0.78 0.79 0.8 0.81 0.82 0.83 0.84 0.85 0.86 0.87 0.88 0.89 0.9 0.91 0.92 0.93 0.94 0.95 0.96 0.97 0.98 0.99 1.
diff --git a/data/tiny_betas.txt b/data/tiny_betas.txt
deleted file mode 100644
index 51e8d2f..0000000
--- a/data/tiny_betas.txt
+++ /dev/null
@@ -1 +0,0 @@
-0.00464534 0.00390625 0.00328475 0.00276214 0.00232267 0.00195313 0.00164238 0.00138107 0.00116134 0.000976563 0.000821188 0.000690534 0.000580668 0.000488281 0.000410594 0.000345267 0.000290334 0.000244141 0.000205297 0.000172633
diff --git a/src/bound_set.c b/lib/bound_set.c
index 65f1e6f..65f1e6f 100644
--- a/src/bound_set.c
+++ b/lib/bound_set.c
diff --git a/src/break_edge.c b/lib/break_edge.c
index 2f112c2..2f112c2 100644
--- a/src/break_edge.c
+++ b/lib/break_edge.c
diff --git a/lib/correlations.c b/lib/correlations.c
new file mode 100644
index 0000000..63532ec
--- /dev/null
+++ b/lib/correlations.c
@@ -0,0 +1,47 @@
+
+#include "fracture.h"
+
+double *get_corr(net_t *instance, uint_t **dists, cholmod_common *c) {
+	uint_t nv = instance->graph->dnv;
+	uint_t ne = instance->graph->ne;
+	uint_t *ev = instance->graph->dev;
+	bool nulldists = false;
+	if (dists == NULL) {
+		dists = graph_dists(instance->graph, false);
+		nulldists = true;
+	}
+	double *corr = calloc(nv, sizeof(double));
+	uint_t *numat = calloc(nv, sizeof(uint_t));
+
+	for (uint_t i = 0; i < ne; i++) {
+		uint_t v1 = ev[2 * i];
+		uint_t v2 = ev[2 * i + 1];
+		for (uint_t j = 0; j < ne; j++) {
+			uint_t v3 = ev[2 * j];
+			uint_t v4 = ev[2 * j + 1];
+			uint_t dist1 = dists[v1][v3];
+			uint_t dist2 = dists[v1][v4];
+			uint_t dist3 = dists[v2][v3];
+			uint_t dist4 = dists[v2][v4];
+			uint_t dist = (dist1 + dist2 + dist3 + dist4) / 4;
+			corr[dist] += instance->fuses[i] && instance->fuses[j];
+			numat[dist]++;
+		}
+	}
+
+	for (uint_t i = 0; i < nv; i++) {
+		if (numat[i] > 0) {
+			corr[i] /= numat[i];
+		}
+	}
+
+	if (nulldists) {
+		for (int i = 0; i < nv; i++) {
+			free(dists[i]);
+		}
+		free(dists);
+	}
+
+	return corr;
+}
+
diff --git a/src/data.c b/lib/data.c
index 2047c44..2047c44 100644
--- a/src/data.c
+++ b/lib/data.c
diff --git a/src/factor_update.c b/lib/factor_update.c
index a51705a..a51705a 100644
--- a/src/factor_update.c
+++ b/lib/factor_update.c
diff --git a/lib/fracture.h b/lib/fracture.h
new file mode 100644
index 0000000..b1114fb
--- /dev/null
+++ b/lib/fracture.h
@@ -0,0 +1,123 @@
+
+#pragma once
+
+#include <assert.h>
+#include <cholmod.h>
+#include <float.h>
+#include <getopt.h>
+#include <gsl/gsl_math.h>
+#include <gsl/gsl_randist.h>
+#include <gsl/gsl_rng.h>
+#include <gsl/gsl_sf_erf.h>
+#include <gsl/gsl_sf_exp.h>
+#include <gsl/gsl_sf_log.h>
+#include <inttypes.h>
+#include <math.h>
+#include <omp.h>
+#include <stdbool.h>
+#include <stdint.h>
+#include <stdio.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <sys/types.h>
+#include <unistd.h>
+
+#include <jst/graph.h>
+#include <jst/rand.h>
+
+
+// these defs allow me to switch to long int cholmod in a sitch
+#define int_t int
+#define uint_t unsigned int
+#define CINT_MAX INT_MAX
+#define CHOL_F(x) cholmod_##x
+
+#define GSL_RAND_GEN gsl_rng_mt19937
+
+typedef struct {
+	const graph_t *graph;
+	bool *fuses;
+	long double *thres;
+	double inf;
+	cholmod_dense *boundary_cond;
+	cholmod_factor *factor;
+	bool voltage_bound;
+	uint_t num_broken;
+	uint_t dim;
+	uint_t nep;
+	uint_t *evp;
+	cholmod_sparse *voltcurmat;
+} net_t;
+
+typedef struct {
+	uint_t num_broken;
+	uint_t *break_list;
+	double *conductivity;
+	long double *extern_field;
+} data_t;
+
+intptr_t *run_voronoi(uint_t num_coords, double *coords, bool periodic, double xmin, double xmax, double ymin, double ymax);
+
+cholmod_sparse *gen_adjacency(const net_t *net, bool dual, bool use_gp, bool symmetric, cholmod_common *c);
+
+cholmod_sparse *gen_laplacian(const net_t *net, cholmod_common *c);
+
+int edge_to_verts(uint_t width, bool periodic, uint_t edge,
+									bool index);
+
+int dual_edge_to_verts(uint_t width, bool periodic, uint_t edge,
+											 bool index);
+
+double dual_vert_to_coord(uint_t width, bool periodic, uint_t vert,
+													bool index);
+
+void factor_update(cholmod_factor *factor, uint_t v1, uint_t v2, cholmod_common *c);
+void factor_update2(cholmod_factor *factor, uint_t v1, cholmod_common *c);
+
+void net_notch(net_t *net, double notch_len, cholmod_common *c);
+data_t *net_fracture(net_t *net, cholmod_common *c, double cutoff);
+double *net_voltages(const net_t *net, cholmod_common *c);
+double *net_currents(const net_t *net, const double *voltages, cholmod_common *c);
+double net_conductivity(const net_t *net, const double *voltages);
+
+void update_boundary(net_t *instance, const double *avg_field);
+
+FILE *get_file(const char *prefix, uint_t width, uint_t crack,
+							 double beta, uint_t iter, uint_t num_iter,
+							 uint_t num, bool read);
+
+double update_beta(double beta, uint_t width, const double *stress,
+									 const double *damage, double bound_total);
+
+cholmod_sparse *gen_voltcurmat(uint_t num_edges, uint_t num_verts,
+															 uint_t *edges_to_verts, cholmod_common *c);
+
+net_t *net_copy(const net_t *net, cholmod_common *c);
+
+void net_free(net_t *instance, cholmod_common *c);
+
+net_t *net_create(const graph_t *g, double inf, double beta, double notch_len, bool vb, cholmod_common *c);
+
+bool break_edge(net_t *instance, uint_t edge, cholmod_common *c);
+
+components_t *get_clusters(net_t *instance);
+
+uint_t *get_cluster_dist(net_t *instance);
+
+void randfunc_flat(gsl_rng *r, double *x, double *y);
+void randfunc_gaus(gsl_rng *r, double *x, double *y);
+
+double *get_corr(net_t *instance, uint_t **dists, cholmod_common *c);
+
+double *bin_values(graph_t *network, uint_t width, double *values);
+
+cholmod_dense *bound_set(const graph_t *g, bool vb, double notch_len, cholmod_common *c);
+
+data_t *data_create(uint_t num_edges);
+void data_free(data_t *data);
+void data_update(data_t *data, uint_t last_broke, long double strength, double conductivity);
+
+long double rand_dist_pow(const gsl_rng *r, double beta);
+
+bool is_in(uint_t len, uint_t *list, uint_t element);
diff --git a/src/gen_laplacian.c b/lib/gen_laplacian.c
index 1cc93a4..1cc93a4 100644
--- a/src/gen_laplacian.c
+++ b/lib/gen_laplacian.c
diff --git a/src/gen_voltcurmat.c b/lib/gen_voltcurmat.c
index e870140..e870140 100644
--- a/src/gen_voltcurmat.c
+++ b/lib/gen_voltcurmat.c
diff --git a/src/geometry.c b/lib/geometry.c
index ec788f1..ec788f1 100644
--- a/src/geometry.c
+++ b/lib/geometry.c
diff --git a/lib/get_dual_clusters.c b/lib/get_dual_clusters.c
new file mode 100644
index 0000000..eaf7562
--- /dev/null
+++ b/lib/get_dual_clusters.c
@@ -0,0 +1,30 @@
+
+#include "fracture.h"
+
+components_t *get_clusters(net_t *instance) {
+	components_t *c = graph_components_get(instance->graph, instance->fuses, true);
+	return c;
+}
+
+unsigned int *get_cluster_dist(net_t *instance) {
+	components_t *c = get_clusters(instance);
+	unsigned int *cluster_dist = (unsigned int *)calloc(
+			instance->graph->dnv, sizeof(unsigned int));
+
+	for (uint32_t i = 1; i <= c->n; i++) {
+		unsigned int num_in_cluster = 0;
+		for (unsigned int j = 0; j < instance->graph->dnv; j++) {
+			if (c->labels[j] == i)
+				num_in_cluster++;
+		}
+
+		if (num_in_cluster == 0)
+			break;
+
+		cluster_dist[num_in_cluster - 1]++;
+	}
+
+	graph_components_free(c);
+
+	return cluster_dist;
+}
diff --git a/src/net.c b/lib/net.c
index a1047e2..d26b22c 100644
--- a/src/net.c
+++ b/lib/net.c
@@ -6,7 +6,7 @@ long double *get_thres(uint_t ne, double beta) {
 	assert(thres != NULL);
 
 	gsl_rng *r = gsl_rng_alloc(GSL_RAND_GEN);
-	gsl_rng_set(r, rand_seed());
+	gsl_rng_set(r, jst_rand_seed());
 
 	for (uint_t i = 0; i < ne; i++) {
 		thres[i] = rand_dist_pow(r, beta);
@@ -102,6 +102,8 @@ net_t *net_create(const graph_t *g, double inf, double beta, double notch_len, b
 		CHOL_F(free_sparse)(&laplacian, c);
 	}
 
+	net->voltcurmat = gen_voltcurmat(g->ne, g->nv, g->ev, c);
+
 	return net;
 }
 
@@ -127,6 +129,7 @@ net_t *net_copy(const net_t *net, cholmod_common *c) {
 
 	net_copy->boundary_cond = CHOL_F(copy_dense)(net->boundary_cond, c);
 	net_copy->factor = CHOL_F(copy_factor)(net->factor, c);
+	net_copy->voltcurmat = CHOL_F(copy_sparse)(net->voltcurmat, c);
 
 	return net_copy;
 }
@@ -136,6 +139,7 @@ void net_free(net_t *net, cholmod_common *c) {
 	free(net->thres);
 	CHOL_F(free_dense)(&(net->boundary_cond), c);
 	CHOL_F(free_factor)(&(net->factor), c);
+	CHOL_F(free_sparse)(&(net->voltcurmat), c);
 	free(net->evp);
 	free(net);
 }
diff --git a/src/net_conductivity.c b/lib/net_conductivity.c
index e9325bb..e9325bb 100644
--- a/src/net_conductivity.c
+++ b/lib/net_conductivity.c
diff --git a/src/net_currents.c b/lib/net_currents.c
index 9bb2874..a078336 100644
--- a/src/net_currents.c
+++ b/lib/net_currents.c
@@ -4,7 +4,7 @@
 double *net_currents(const net_t *net, const double *voltages, cholmod_common *c) {
 	uint_t ne = net->graph->ne;
 	uint_t dim = net->graph->nv;
-	cholmod_sparse *voltcurmat = net->graph->voltcurmat;
+	cholmod_sparse *voltcurmat = net->voltcurmat;
 
 	cholmod_dense *x = CHOL_F(allocate_dense)(dim, 1, dim, CHOLMOD_REAL, c);
 
diff --git a/src/net_fracture.c b/lib/net_fracture.c
index e7f18fc..e7f18fc 100644
--- a/src/net_fracture.c
+++ b/lib/net_fracture.c
diff --git a/src/net_voltages.c b/lib/net_voltages.c
index c3537a5..7b07201 100644
--- a/src/net_voltages.c
+++ b/lib/net_voltages.c
@@ -16,7 +16,7 @@ double *net_voltages(const net_t *net, cholmod_common *c) {
 	x->x = NULL;
 	CHOL_F(free_dense)(&x, c);
 
-	graph_t *g = net->graph;
+	const graph_t *g = net->graph;
 
 	if (g->boundary == TORUS_BOUND) {
 		return t_voltages;
diff --git a/src/rand.c b/lib/rand.c
index 75722ac..16aeba4 100644
--- a/src/rand.c
+++ b/lib/rand.c
@@ -1,14 +1,6 @@
 
 #include "fracture.h"
 
-unsigned long int rand_seed() {
-	FILE *f = fopen("/dev/urandom", "r");
-	unsigned long int seed;
-	fread(&seed, sizeof(unsigned long int), 1, f);
-	fclose(f);
-	return seed;
-}
-
 long double rand_dist_pow(const gsl_rng *r, double beta) {
 	long double x = 0;
 
diff --git a/makefile b/makefile
deleted file mode 100644
index 9ea3865..0000000
--- a/makefile
+++ /dev/null
@@ -1,45 +0,0 @@
-
-CC = clang
-CCP = clang++
-CFLAGS = -g -Os -O3 -Wall -fno-strict-aliasing -Wstrict-overflow -Wno-missing-field-initializers -fPIC -flto -fopenmp -march=native 
-CPFLAGS = -g -Os -O3 -Wall -fno-strict-aliasing -Wstrict-overflow -Wno-missing-field-initializers -fPIC -flto -fopenmp -march=native 
-CCPFLAGS = -g -Os -O3 -Wall -fno-strict-aliasing -Wstrict-overflow -Wno-missing-field-initializers -fPIC -flto -shared -fopenmp -march=native 
-LDFLAGS = -lc -lcblas -llapack -ldl -lpthread -lcholmod -lamd -lcolamd -lsuitesparseconfig -lcamd -lccolamd -lm -lrt -lmetis -lgsl -lprofiler -ltcmalloc
-
-OBJ = data bound_set correlations factor_update graph_genfunc net net_voltages net_currents net_conductivity net_fracture get_dual_clusters break_edge graph_components gen_laplacian geometry gen_voltcurmat graph_create graph_free fortune/edgelist fortune/geometry fortune/heap fortune/main fortune/output fortune/voronoi fortune/memory rand frame_create
-OBJP = spheres_poly/box spheres_poly/event spheres_poly/heap spheres_poly/neighbor spheres_poly/sphere
-OBJCCP = spheres_poly/spheres
-BIN = corr_test fracture anal_process big_anal_process cen_anal_process long_anal_process
-
-
-all: opt ${OBJ:%=obj/%.o} ${OBJP:%=obj/%.o} ${BIN:%=obj/%.o} ${BIN:%=bin/%}
-
-opt:
-	@echo build options:
-	@echo "CC       = ${CC}"
-	@echo "CFLAGS   = ${CFLAGS}"
-	@echo "LDFLAGS  = ${LDFLAGS}"
-
-${OBJ:%=obj/%.o} ${BIN:%=obj/%.o}: obj/%.o: src/%.c
-	@echo CC -c -o $@
-	@${CC} -c ${CFLAGS} $< -o $@
-
-${OBJP:%=obj/%.o}: obj/%.o: src/%.cpp
-	@echo CCP -c -o $@
-	@${CCP} -c ${CPFLAGS} $< -o $@
-
-${OBJCCP:%=obj/%.o}: obj/%.o: src/%.cpp ${OBJP:%=obj/%.o} 
-	@echo ${CCP} ${CCPFLAGS} ${OBJP:%=obj/%.o} $< -o $@
-	@${CCP} ${CCPFLAGS} ${OBJP:%=obj/%.o} -fuse-ld=gold $< -o $@
-
-bin/%: obj/%.o ${OBJ:%=obj/%.o} ${OBJCCP:%=obj/%.o} src/fracture.h
-	@echo ${CC} ${OBJ:%=obj/%.o} ${OBJCCP:%=obj/%.o} -fuse-ld=gold ${CFLAGS} ${LDFLAGS} $< -o $@
-	@${CC} ${OBJ:%=obj/%.o} ${OBJCCP:%=obj/%.o} -fuse-ld=gold ${CFLAGS} ${LDFLAGS} $< -o $@
-
-clean:
-	@echo cleaning:
-	@echo rm -f ${OBJ:%=obj/%.o} ${OBJP:%=obj/%.o} ${OBJCCP:%=obj/%.o} ${BIN:%=obj/%.o} ${BIN:%=bin/%}
-	@rm -f ${OBJ:%=obj/%.o} ${OBJP:%=obj/%.o} ${OBJCCP:%=obj/%.o} ${BIN:%=obj/%.o} ${BIN:%=bin/%}
-
-.PHONY: all clean
-
diff --git a/src/corr_test.c b/src/corr_test.c
index b6f8a18..01b3e11 100644
--- a/src/corr_test.c
+++ b/src/corr_test.c
@@ -7,7 +7,7 @@ int main() {
 
 	unsigned int width = 64;
 
-	graph_t *network = graph_create(VORONOI_LATTICE, TORUS_BOUND, 128, false, &c);
+	graph_t *network = graph_create(VORONOI_LATTICE, TORUS_BOUND, 128, false);
 	net_t *instance = net_create(network, 1e-14, 3, 0, true, &c);
 	net_fracture(instance, &c, 1e-10);
 
@@ -19,7 +19,7 @@ int main() {
 	printf("\n");
 
 	net_free(instance, &c);
-	graph_free(network, &c);
+	graph_free(network);
 
 	CHOL_F(finish)(&c);
 
diff --git a/src/correlations.c b/src/correlations.c
deleted file mode 100644
index f403ab8..0000000
--- a/src/correlations.c
+++ /dev/null
@@ -1,299 +0,0 @@
-
-#include "fracture.h"
-
-// I implemented a fibonacci heap because wikipedia said it would be fast
-
-struct fibn {
-	uint_t value;
-	uint_t priority;
-	uint_t rank;
-	bool marked;
-	struct fibn *first_child;
-	struct fibn *parent;
-	struct fibn *prev;
-	struct fibn *next;
-};
-
-typedef struct {
-	struct fibn *min;
-	uint_t rank;
-	uint_t trees;
-	struct fibn **vertex_to_node;
-} fibh;
-
-uint_t fib_findmin(fibh *heap) {
-	return heap->min->value;
-}
-
-void ll_setparent(struct fibn *ll, struct fibn *parent) {
-	struct fibn *curnode = ll->next;
-	ll->parent = parent;
-	while (curnode != ll) {
-		curnode->parent = parent;
-		curnode = curnode->next;
-	}
-}
-
-struct fibn *ll_merge(struct fibn *ll1, struct fibn *ll2) {
-	if (ll1 == NULL)
-		return ll2;
-	if (ll2 == NULL)
-		return ll1;
-
-	// link the beginning of list one to the end of list two and vice versa
-	struct fibn *ll1_beg = ll1;
-	struct fibn *ll1_end = ll1->prev;
-	struct fibn *ll2_beg = ll2;
-	struct fibn *ll2_end = ll2->prev;
-
-	ll1_beg->prev = ll2_end;
-	ll1_end->next = ll2_beg;
-	ll2_beg->prev = ll1_end;
-	ll2_end->next = ll1_beg;
-
-	return ll1;
-}
-
-struct fibn *ll_delroot(struct fibn *ll) {
-	if (ll == NULL)
-		return NULL;
-
-	if (ll->next == ll) {
-		return NULL;
-	}
-
-	struct fibn *ll_beg = ll->next;
-	struct fibn *ll_end = ll->prev;
-
-	ll_beg->prev = ll_end;
-	ll_end->next = ll_beg;
-
-	ll->next = ll;
-	ll->prev = ll;
-
-	return ll_beg;
-}
-
-void fib_insert(fibh *heap, uint_t value, uint_t priority) {
-	struct fibn *newnode = calloc(1, sizeof(struct fibn));
-	newnode->value = value;
-	newnode->priority = priority;
-	newnode->next = newnode;
-	newnode->prev = newnode;
-
-	heap->min = ll_merge(heap->min, newnode);
-
-	if (priority < heap->min->priority) {
-		heap->min = newnode;
-	}
-
-	heap->vertex_to_node[value] = newnode;
-
-	heap->trees++;
-}
-
-void fib_deletemin(fibh *heap) {
-	uint_t min_rank = heap->min->rank;
-	struct fibn *min_children = heap->min->first_child;
-
-	struct fibn *trees = ll_delroot(heap->min);
-	heap->vertex_to_node[heap->min->value] = NULL;
-	free(heap->min);
-
-	if (min_children != NULL)
-		ll_setparent(min_children, NULL);
-	trees = ll_merge(trees, min_children);
-
-	heap->trees += min_rank - 1;
-
-	if (trees == NULL) {
-		// min had no children and was only tree, return empty heap
-		heap->min = NULL;
-		heap->rank = 0;
-	} else {
-		// min had children or there were other trees
-		uint_t min_val = UINT_MAX;
-		struct fibn *min_ptr = NULL;
-		uint_t max_rank = 0;
-		struct fibn *curnode = trees;
-		for (uint_t i = 0; i < heap->trees; i++) {
-			if (curnode->priority < min_val) {
-				min_ptr = curnode;
-				min_val = curnode->priority;
-			}
-			if (curnode->rank > max_rank)
-				max_rank = curnode->rank;
-			curnode = curnode->next;
-		}
-
-		if (min_ptr == NULL)
-			min_ptr = trees;
-		heap->min = min_ptr;
-		heap->rank = max_rank;
-
-		struct fibn **rankslots = calloc(max_rank + 1, sizeof(struct fibn *));
-		curnode = heap->min;
-		while (curnode != rankslots[curnode->rank]) {
-			if (rankslots[curnode->rank] == NULL) {
-				rankslots[curnode->rank] = curnode;
-				curnode = curnode->next;
-			} else {
-				struct fibn *oldnode = rankslots[curnode->rank];
-				rankslots[curnode->rank] = NULL;
-				struct fibn *smaller =
-						curnode->priority < oldnode->priority || curnode == heap->min
-								? curnode
-								: oldnode;
-				struct fibn *larger = smaller == curnode ? oldnode : curnode;
-				ll_delroot(larger);
-				ll_setparent(larger, smaller);
-				struct fibn *smaller_children = smaller->first_child;
-				smaller->first_child = ll_merge(smaller_children, larger);
-				heap->trees--;
-				smaller->rank++;
-				if (smaller->rank > heap->rank) {
-					heap->rank = smaller->rank;
-					rankslots =
-							realloc(rankslots, (heap->rank + 1) * sizeof(struct fibn *));
-					rankslots[heap->rank] = NULL;
-				}
-				curnode = smaller;
-			}
-		}
-		free(rankslots);
-	}
-}
-
-void fib_decreasekey(fibh *heap, uint_t value, uint_t new_priority) {
-	struct fibn *node = heap->vertex_to_node[value];
-	if (node != NULL) {
-		node->priority = new_priority;
-		if (node->parent != NULL) {
-			if (node->priority < node->parent->priority) {
-
-				struct fibn *curnode = node;
-				curnode->marked = true;
-				while (curnode->parent != NULL && curnode->marked) {
-					struct fibn *oldparent = curnode->parent;
-					oldparent->rank--;
-					oldparent->first_child = ll_delroot(curnode);
-					ll_setparent(curnode, NULL);
-					ll_merge(heap->min, curnode);
-					heap->trees++;
-					if (curnode->marked) {
-						curnode->marked = false;
-					}
-
-					if (oldparent->marked) {
-						curnode = oldparent;
-					} else {
-						oldparent->marked = true;
-						break;
-					}
-				}
-			}
-		}
-
-		if (new_priority < heap->min->priority) {
-			heap->min = node;
-		}
-	}
-}
-
-uint_t *dijkstra(const graph_t *network, uint_t source) {
-	uint_t nv = network->dnv;
-	uint_t *vei = network->dvei;
-	uint_t *ve = network->dve;
-	uint_t *ev = network->dev;
-
-	uint_t *dist = (uint_t *)calloc(nv, sizeof(uint_t));
-	fibh *Q = (fibh *)calloc(1, sizeof(fibh));
-	Q->vertex_to_node = (struct fibn **)calloc(nv, sizeof(struct fibn *));
-
-	for (uint_t i = 0; i < nv; i++) {
-		if (i != source) {
-			dist[i] = UINT_MAX;
-		}
-
-		fib_insert(Q, i, dist[i]);
-	}
-
-	while (Q->min != NULL) {
-		uint_t u = fib_findmin(Q);
-		fib_deletemin(Q);
-
-		for (uint_t i = 0; i < vei[u + 1] - vei[u]; i++) {
-			uint_t e = ve[vei[u] + i];
-			uint_t v = ev[2 * e] == u ? ev[2 * e + 1] : ev[2 * e];
-			uint_t alt = dist[u] + 1;
-			if (alt < dist[v]) {
-				dist[v] = alt;
-				fib_decreasekey(Q, v, alt);
-			}
-		}
-	}
-
-	free(Q->vertex_to_node);
-	free(Q);
-
-	return dist;
-}
-
-uint_t **get_dists(const graph_t *network) {
-	uint_t nv = network->dnv;
-	uint_t **dists = (uint_t **)malloc(nv * sizeof(uint_t *));
-
-	for (uint_t i = 0; i < nv; i++) {
-		dists[i] = dijkstra(network, i);
-	}
-
-	return dists;
-}
-
-double *get_corr(net_t *instance, uint_t **dists, cholmod_common *c) {
-	uint_t nv = instance->graph->dnv;
-	uint_t ne = instance->graph->ne;
-	uint_t *ev = instance->graph->dev;
-	bool nulldists = false;
-	if (dists == NULL) {
-		dists = get_dists(instance->graph);
-		nulldists = true;
-	}
-	double *corr = calloc(nv, sizeof(double));
-	uint_t *marks = get_clusters(instance, c);
-	uint_t *numat = calloc(nv, sizeof(uint_t));
-
-	for (uint_t i = 0; i < ne; i++) {
-		uint_t v1 = ev[2 * i];
-		uint_t v2 = ev[2 * i + 1];
-		for (uint_t j = 0; j < ne; j++) {
-			uint_t v3 = ev[2 * j];
-			uint_t v4 = ev[2 * j + 1];
-			uint_t dist1 = dists[v1][v3];
-			uint_t dist2 = dists[v1][v4];
-			uint_t dist3 = dists[v2][v3];
-			uint_t dist4 = dists[v2][v4];
-			uint_t dist = (dist1 + dist2 + dist3 + dist4) / 4;
-			corr[dist] += instance->fuses[i] && instance->fuses[j];
-			numat[dist]++;
-		}
-	}
-
-	for (uint_t i = 0; i < nv; i++) {
-		if (numat[i] > 0) {
-			corr[i] /= numat[i];
-		}
-	}
-
-	if (nulldists) {
-		for (int i = 0; i < nv; i++) {
-			free(dists[i]);
-		}
-		free(dists);
-	}
-
-	free(marks);
-
-	return corr;
-}
-
diff --git a/src/fitting_functions.c b/src/fitting_functions.c
deleted file mode 100644
index aa7a305..0000000
--- a/src/fitting_functions.c
+++ /dev/null
@@ -1,290 +0,0 @@
-
-#include "fracture.h"
-#include <gsl/gsl_sf_erf.h>
-#include <gsl/gsl_sf_laguerre.h>
-#include <gsl/gsl_matrix.h>
-#include <gsl/gsl_vector.h>
-#include <gsl/gsl_blas.h>
-#include <gsl/gsl_multifit_nlinear.h>
-
-struct model_params {
-	double nu;
-	double ac;
-	double mc;
-	double ac02;
-	double ac03;
-	double ac12;
-	double ac13;
-	double bc02;
-	double bc03;
-	double bc12;
-	double bc13;
-	double Ac20;
-	double Ac21;
-	double Ac22;
-	double Ac23;
-	double Ac30;
-	double Ac31;
-	double Ac32;
-	double Ac33;
-	double Bc20;
-	double Bc21;
-	double Bc22;
-	double Bc23;
-	double Bc30;
-	double Bc31;
-	double Bc32;
-	double Bc33;
-};
-
-struct data {
-	uint_t nc;
-	uint_t *Ls_c;
-	double *betas_c;
-	double *vals_c2;
-	double *vals_c3;
-};
-
-double Jc(uint_t n, uint_t o, struct model_params *par, double x) {
-	double nu, ac, mc, ac0n, bc0n, *Acn, yc, sum;
-
-	nu = par->nu;
-	ac = par->ac;
-	mc = par->mc;
-	ac0n = *(&(par->ac02) + (n - 2) * sizeof(double));
-	bc0n = *(&(par->bc02) + (n - 2) * sizeof(double));
-	Acn = &(par->Ac20) + (n - 2) * o * sizeof(double);
-
-	yc = (log(x) - mc) / ac;
-
-	sum = 0;
-
-	for (uint_t i = 0; i < o; i++) {
-		sum += Acn[i] * gsl_sf_laguerre_n(i, 0, yc);
-	}
-
-	return exp(ac0n + bc0n * (2 - gsl_sf_erf(yc)) + exp(-gsl_pow_2(yc)) * sum);
-}
-
-double Kc(uint_t n, uint_t o, struct model_params *par, double x) {
-	double nu, ac, mc, ac1n, bc1n, *Bcn, yc, sum;
-
-	nu = par->nu;
-	ac = par->ac;
-	mc = par->mc;
-	ac1n = *(&(par->ac12) + (n - 2) * sizeof(double));
-	bc1n = *(&(par->bc12) + (n - 2) * sizeof(double));
-	Bcn = &(par->Bc20) + (n - 2) * o * sizeof(double);
-
-	yc = (log(x) - mc) / ac;
-
-	sum = 0;
-
-	for (uint_t i = 0; i < o; i++) {
-		sum += Bcn[i] * gsl_sf_laguerre_n(i, 0, yc);
-	}
-
-	return exp(ac1n + bc1n * (2 - gsl_sf_erf(yc)) + exp(-gsl_pow_2(yc)) * sum);
-}
-
-double sc(uint_t n, uint_t o, struct model_params *par, uint_t L, double beta) {
-	double nu, bLnu, deltanu, sigmanu, tau, Lntau, Ldelta;
-
-	nu = par->nu;
-	deltanu = 1.5;
-	sigmanu = 48. / 91;
-	tau = 187. / 91;
-
-	bLnu = beta * exp(log(L) / nu);
-	Lntau = exp((n + 1 - tau) / sigmanu * log(L));
-	Ldelta = exp(-deltanu * log(L));
-
-	return Lntau * (Jc(n, o, par, bLnu) + Ldelta * Kc(n, 0, par, bLnu));
-}
-
-int f_moms(const gsl_vector *x, void *params, gsl_vector *f) {
-	struct data *dat = (struct data *)params;
-
-	for (uint_t i = 0; i < dat->nc; i++) {
-		double f2i = sc(2, 4, (struct model_params *)x->data, dat->Ls_c[i], dat->betas_c[i]);
-		double F2i = dat->vals_c2[i];
-
-		f2i = log(f2i);
-		F2i = log(F2i);
-
-		gsl_vector_set(f, i, f2i - F2i);
-
-		double f3i = sc(3, 4, (struct model_params *)x->data, dat->Ls_c[i], dat->betas_c[i]);
-		double F3i = dat->vals_c3[i];
-
-		f3i = log(f3i);
-		F3i = log(F3i);
-
-		gsl_vector_set(f, dat->nc + i, f3i - F3i);
-	}
-
-	return GSL_SUCCESS;
-}
-
-void mom(uint_t len, uint_t n, uint32_t *data, double result[2]) {
-	uint_t total = 0;
-	double mom = 0;
-	double mom_err = 0;
-
-	for (uint_t i = 0; i < len; i++) {
-		uint32_t datai = data[i];
-		double in = pow(i, n);
-
-		total += datai;
-		mom += in * datai;
-		mom_err += gsl_pow_2(in) * datai; 
-	}
-
-	double momf = mom / total;
-	double momf_err = momf * sqrt(mom_err / gsl_pow_2(mom) + 1 / total);
-
-	result[0] = momf;
-	result[1] = momf_err;
-}
-
-void
-callback(const size_t iter, void *params,
-         const gsl_multifit_nlinear_workspace *w)
-{
-  gsl_vector *f = gsl_multifit_nlinear_residual(w);
-
-  fprintf(stderr, "iter %2zu: |f(x)| = %.4f\n",
-          iter,
-          gsl_blas_dnrm2(f));
-}
-
-
-int main(int argc, char *argv[]) {
-	struct data *d = (struct data *)malloc(sizeof(struct data));
-	uint_t nc = argc - 1;
-	uint_t *Ls_c = (uint_t *)malloc(nc * sizeof(uint_t));
-	double *betas_c = (double *)malloc(nc * sizeof(double));
-	double *vals_c2 = (double *)malloc(nc * sizeof(double));
-	double *weights_c2 = (double *)malloc(nc * sizeof(double));
-	double *vals_c3 = (double *)malloc(nc * sizeof(double));
-	double *weights_c3 = (double *)malloc(nc * sizeof(double));
-
-	double chisq, chisq0;
-
-	d->nc = nc;
-	d->Ls_c = Ls_c;
-	d->betas_c = betas_c;
-	d->vals_c2 = vals_c2;
-	d->vals_c3 = vals_c3;
-
-	for (uint_t i = 0; i < nc; i++) {
-		char *fn = argv[1 + i];
-		char *buff = malloc(20 * sizeof(char));
-		uint_t pos = 0; uint_t c = 0;
-		while (c < 4) {
-			if (fn[pos] == '_') {
-				c++;
-			}
-			pos++;
-		}
-		c = 0;
-		while (fn[pos] != '_') {
-			buff[c] = fn[pos];
-			pos++;
-			c++;
-		}
-		buff[c] = '\0';
-		Ls_c[i] = atoi(buff);
-		c = 0;
-		pos++;
-		while (fn[pos] != '_') {
-			buff[c] = fn[pos];
-			pos++;
-			c++;
-		}
-		buff[c] = '\0';
-		betas_c[i] = atof(buff);
-		free(buff);
-
-		uint_t dist_len = 4 * pow(Ls_c[i], 2);
-		uint32_t *dist = malloc(dist_len * sizeof(uint32_t));
-		FILE *dist_file = fopen(fn, "rb");
-		fread(dist, sizeof(uint32_t), dist_len, dist_file);
-		fclose(dist_file);
-		{
-			double mom2[2];
-			mom(dist_len, 2, dist, mom2);
-			vals_c2[i] = mom2[0];
-			weights_c2[i] = mom2[1];
-
-			double mom3[2];
-			mom(dist_len, 3, dist, mom3);
-			vals_c3[i] = mom3[0];
-			weights_c3[i] = mom3[1];
-		}
-		free(dist);
-	}
-
-	const gsl_multifit_nlinear_type *T = gsl_multifit_nlinear_trust;
-	gsl_multifit_nlinear_workspace *w;
-	gsl_multifit_nlinear_fdf fdf;
-	gsl_multifit_nlinear_parameters fdf_params = gsl_multifit_nlinear_default_parameters();
-	uint_t n = 2 * nc;
-	uint_t p = 27;
-
-	double x_init[27] = { 1.56, .3, 2, -6, -10, -10, -10, 10, 15, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 };
-	double weights[n];
-	for (uint_t i = 0; i < nc; i++) {
-		weights[i] = 1/gsl_pow_2(weights_c2[i] / vals_c2[i]);
-		weights[nc + i] = 1/gsl_pow_2(weights_c3[i] / vals_c3[i]);
-	}
-
-	gsl_vector_view x = gsl_vector_view_array(x_init, p);
-	gsl_vector_view wts = gsl_vector_view_array(weights, n);
-
-	gsl_vector *f;
-
-	fdf.f = f_moms;
-	fdf.df = NULL;
-	fdf.fvv = NULL;
-	fdf.n = n;
-	fdf.p = p;
-	fdf.params = d;
-
-	fdf_params.trs = gsl_multifit_nlinear_trs_lm;
-
-	w = gsl_multifit_nlinear_alloc(T, &fdf_params, n, p);
-	gsl_multifit_nlinear_winit(&x.vector, &wts.vector, &fdf, w);
-	f = gsl_multifit_nlinear_residual(w);
-	gsl_blas_ddot(f, f, &chisq0);
-
-	const double xtol = 0.0;
-	const double gtol = 0.0;
-	const double ftol = 0.0;
-
-	int info;
-	int status = gsl_multifit_nlinear_driver(100, xtol, gtol, ftol, callback, NULL, &info, w);
-	gsl_blas_ddot(f, f, &chisq);
-
-	fprintf(stderr, "summary from method '%s/%s'\n",
-			          gsl_multifit_nlinear_name(w),
-								          gsl_multifit_nlinear_trs_name(w));
-
-	fprintf(stderr, "number of iterations: %zu\n",
-			          gsl_multifit_nlinear_niter(w));
-	  fprintf(stderr, "function evaluations: %zu\n", fdf.nevalf);
-			  fprintf(stderr, "reason for stopping: %s\n",
-						          (info == 1) ? "small step size" : "small gradient");
-				  fprintf(stderr, "initial |f(x)| = %g\n", sqrt(chisq0));
-					  fprintf(stderr, "final   |f(x)| = %g\n", sqrt(chisq));
-
-	free(Ls_c);
-	free(betas_c);
-	free(vals_c2);
-	free(weights_c2);
-	free(vals_c3);
-	free(weights_c3);
-
-	return 0;
-}
-
diff --git a/src/fortune/defs.h b/src/fortune/defs.h
deleted file mode 100644
index 9f1b1db..0000000
--- a/src/fortune/defs.h
+++ /dev/null
@@ -1,134 +0,0 @@
-#ifndef NULL
-#define NULL 0
-#endif
-#define DELETED -2
-#include <stdlib.h>
-#include <limits.h>
-#include <stdbool.h>
-
-extern int triangulate, sorted, plot, debug;
-
-struct Freenode {
-	struct Freenode *nextfree;
-};
-struct Freelist {
-	struct Freenode *head;
-	int nodesize;
-};
-char *getfree();
-char *myalloc();
-
-extern double xmin, xmax, ymin, ymax, deltax, deltay;
-
-struct Point {
-	double x, y;
-};
-
-/* structure used both for sites and for vertices */
-struct Site {
-	struct Point coord;
-	int sitenbr;
-	int refcnt;
-};
-
-extern struct Site *sites;
-extern int nsites;
-extern int siteidx;
-extern int sqrt_nsites;
-extern int nvertices;
-extern struct Freelist sfl;
-extern struct Site *bottomsite;
-
-void **alloclist;
-int allocnum;
-
-struct Edge {
-	double a, b, c;
-	struct Site *ep[2];
-	struct Site *reg[2];
-	int edgenbr;
-};
-#define le 0
-#define re 1
-extern int nedges;
-extern struct Freelist efl;
-
-int has_endpoint(), right_of();
-struct Site *intersect();
-double dist();
-struct Point PQ_min();
-struct Halfedge *PQextractmin();
-struct Edge *bisect();
-
-struct Halfedge {
-	struct Halfedge *ELleft, *ELright;
-	struct Edge *ELedge;
-	int ELrefcnt;
-	char ELpm;
-	struct Site *vertex;
-	double ystar;
-	struct Halfedge *PQnext;
-};
-
-extern struct Freelist hfl;
-extern struct Halfedge *ELleftend, *ELrightend;
-extern int ELhashsize;
-extern struct Halfedge **ELhash;
-struct Halfedge *HEcreate(), *ELleft(), *ELright(), *ELleftbnd();
-struct Site *leftreg(), *rightreg();
-
-extern int PQhashsize;
-extern struct Halfedge *PQhash;
-extern struct Halfedge *PQfind();
-extern int PQcount;
-extern int PQmin;
-int PQempty();
-
-extern double *site_list;
-extern double *vert_list;
-extern double *line_list;
-extern unsigned int *edge_list;
-extern unsigned int *dual_list;
-
-extern int vert_count;
-extern int edge_count;
-extern int line_count;
-extern int dual_count;
-extern int site_count;
-
-void makefree(struct Freenode *curr, struct Freelist *fl);
-void voronoi(int triangulate, struct Site *(*nextsite)());
-char *getfree(struct Freelist *fl);
-char *myalloc(unsigned n);
-void freeinit(struct Freelist *fl, int size);
-void ELinitialize();
-struct Halfedge *HEcreate(struct Edge *e, int pm);
-void ELinsert(struct Halfedge *lb, struct Halfedge *new);
-struct Halfedge *ELgethash(int b);
-struct Halfedge *ELleftbnd(struct Point *p);
-void ELdelete(struct Halfedge *he);
-struct Halfedge *ELright(struct Halfedge *he);
-struct Halfedge *ELleft(struct Halfedge *he);
-struct Site *leftreg(struct Halfedge *he);
-struct Site *rightreg(struct Halfedge *he);
-void geominit();
-struct Edge *bisect(struct Site *s1, struct Site *s2);
-struct Site *intersect(struct Halfedge *el1, struct Halfedge *el2);
-int right_of(struct Halfedge *el, struct Point *p);
-void endpoint(struct Edge *e, int lr, struct Site *s);
-double dist(struct Site *s, struct Site *t);
-void makevertex(struct Site *v);
-void deref(struct Site *v);
-void ref(struct Site *v);
-void PQinsert(struct Halfedge *he, struct Site *v, double offset);
-void PQdelete(struct Halfedge *he);
-int PQbucket(struct Halfedge *he);
-int PQempty();
-struct Point PQ_min();
-struct Halfedge *PQextractmin();
-void PQinitialize();
-void out_bisector(struct Edge *e);
-void out_ep(struct Edge *e);
-void out_vertex(struct Site *v);
-void out_site(struct Site *s);
-void out_triple(struct Site *s1, struct Site *s2, struct Site *s3);
diff --git a/src/fortune/edgelist.c b/src/fortune/edgelist.c
deleted file mode 100644
index dfd85a7..0000000
--- a/src/fortune/edgelist.c
+++ /dev/null
@@ -1,136 +0,0 @@
-#
-#include "defs.h"
-int nedges;
-struct Freelist efl;
-struct Freelist hfl;
-struct Halfedge *ELleftend, *ELrightend;
-int ELhashsize;
-struct Halfedge **ELhash;
-
-int ntry, totalsearch;
-
-void ELinitialize() {
-	int i;
-	freeinit(&hfl, sizeof **ELhash);
-	ELhashsize = 2 * sqrt_nsites;
-	ELhash = (struct Halfedge **)myalloc(sizeof *ELhash * ELhashsize);
-	for (i = 0; i < ELhashsize; i += 1)
-		ELhash[i] = (struct Halfedge *)NULL;
-	ELleftend = HEcreate((struct Edge *)NULL, 0);
-	ELrightend = HEcreate((struct Edge *)NULL, 0);
-	ELleftend->ELleft = (struct Halfedge *)NULL;
-	ELleftend->ELright = ELrightend;
-	ELrightend->ELleft = ELleftend;
-	ELrightend->ELright = (struct Halfedge *)NULL;
-	ELhash[0] = ELleftend;
-	ELhash[ELhashsize - 1] = ELrightend;
-}
-
-struct Halfedge *HEcreate(e, pm) struct Edge *e;
-int pm;
-{
-	struct Halfedge *answer;
-	answer = (struct Halfedge *)getfree(&hfl);
-	answer->ELedge = e;
-	answer->ELpm = pm;
-	answer->PQnext = (struct Halfedge *)NULL;
-	answer->vertex = (struct Site *)NULL;
-	answer->ELrefcnt = 0;
-	return (answer);
-}
-
-void ELinsert(struct Halfedge *lb, struct Halfedge *new) {
-	new->ELleft = lb;
-	new->ELright = lb->ELright;
-	(lb->ELright)->ELleft = new;
-	lb->ELright = new;
-}
-
-/* Get entry from hash table, pruning any deleted nodes */
-struct Halfedge *ELgethash(b) int b;
-{
-	struct Halfedge *he;
-
-	if (b < 0 || b >= ELhashsize)
-		return ((struct Halfedge *)NULL);
-	he = ELhash[b];
-	if (he == (struct Halfedge *)NULL || he->ELedge != (struct Edge *)DELETED)
-		return (he);
-
-	/* Hash table points to deleted half edge.  Patch as necessary. */
-	ELhash[b] = (struct Halfedge *)NULL;
-	if ((he->ELrefcnt -= 1) == 0)
-		makefree((struct Freenode *)he, &hfl);
-	return ((struct Halfedge *)NULL);
-}
-
-struct Halfedge *ELleftbnd(p) struct Point *p;
-{
-	int i, bucket;
-	struct Halfedge *he;
-
-	/* Use hash table to get close to desired halfedge */
-	bucket = (p->x - xmin) / deltax * ELhashsize;
-	if (bucket < 0)
-		bucket = 0;
-	if (bucket >= ELhashsize)
-		bucket = ELhashsize - 1;
-	he = ELgethash(bucket);
-	if (he == (struct Halfedge *)NULL) {
-		for (i = 1; 1; i += 1) {
-			if ((he = ELgethash(bucket - i)) != (struct Halfedge *)NULL)
-				break;
-			if ((he = ELgethash(bucket + i)) != (struct Halfedge *)NULL)
-				break;
-		};
-		totalsearch += i;
-	};
-	ntry += 1;
-	/* Now search linear list of halfedges for the corect one */
-	if (he == ELleftend || (he != ELrightend && right_of(he, p))) {
-		do {
-			he = he->ELright;
-		} while (he != ELrightend && right_of(he, p));
-		he = he->ELleft;
-	} else
-		do {
-			he = he->ELleft;
-		} while (he != ELleftend && !right_of(he, p));
-
-	/* Update hash table and reference counts */
-	if (bucket > 0 && bucket < ELhashsize - 1) {
-		if (ELhash[bucket] != (struct Halfedge *)NULL)
-			ELhash[bucket]->ELrefcnt -= 1;
-		ELhash[bucket] = he;
-		ELhash[bucket]->ELrefcnt += 1;
-	};
-	return (he);
-}
-
-/* This delete routine can't reclaim node, since pointers from hash
-	 table may be present.   */
-void ELdelete(struct Halfedge *he) {
-	(he->ELleft)->ELright = he->ELright;
-	(he->ELright)->ELleft = he->ELleft;
-	he->ELedge = (struct Edge *)DELETED;
-}
-
-struct Halfedge *ELright(he) struct Halfedge *he;
-{ return (he->ELright); }
-
-struct Halfedge *ELleft(he) struct Halfedge *he;
-{ return (he->ELleft); }
-
-struct Site *leftreg(he) struct Halfedge *he;
-{
-	if (he->ELedge == (struct Edge *)NULL)
-		return (bottomsite);
-	return (he->ELpm == le ? he->ELedge->reg[le] : he->ELedge->reg[re]);
-}
-
-struct Site *rightreg(he) struct Halfedge *he;
-{
-	if (he->ELedge == (struct Edge *)NULL)
-		return (bottomsite);
-	return (he->ELpm == le ? he->ELedge->reg[re] : he->ELedge->reg[le]);
-}
diff --git a/src/fortune/geometry.c b/src/fortune/geometry.c
deleted file mode 100644
index 131cacf..0000000
--- a/src/fortune/geometry.c
+++ /dev/null
@@ -1,184 +0,0 @@
-#
-#include "defs.h"
-#include <math.h>
-
-void geominit() {
-	struct Edge e;
-	double sn;
-
-	freeinit(&efl, sizeof e);
-	nvertices = 0;
-	nedges = 0;
-	sn = nsites + 4;
-	sqrt_nsites = sqrt(sn);
-	deltay = ymax - ymin;
-	deltax = xmax - xmin;
-}
-
-struct Edge *bisect(s1, s2) struct Site *s1, *s2;
-{
-	double dx, dy, adx, ady;
-	struct Edge *newedge;
-
-	newedge = (struct Edge *)getfree(&efl);
-
-	newedge->reg[0] = s1;
-	newedge->reg[1] = s2;
-	ref(s1);
-	ref(s2);
-	newedge->ep[0] = (struct Site *)NULL;
-	newedge->ep[1] = (struct Site *)NULL;
-
-	dx = s2->coord.x - s1->coord.x;
-	dy = s2->coord.y - s1->coord.y;
-	adx = dx > 0 ? dx : -dx;
-	ady = dy > 0 ? dy : -dy;
-	newedge->c = s1->coord.x * dx + s1->coord.y * dy + (dx * dx + dy * dy) * 0.5;
-	if (adx > ady) {
-		newedge->a = 1.0;
-		newedge->b = dy / dx;
-		newedge->c /= dx;
-	} else {
-		newedge->b = 1.0;
-		newedge->a = dx / dy;
-		newedge->c /= dy;
-	};
-
-	newedge->edgenbr = nedges;
-	out_bisector(newedge);
-	nedges += 1;
-	return (newedge);
-}
-
-struct Site *intersect(el1, el2) struct Halfedge *el1, *el2;
-{
-	struct Edge *e1, *e2, *e;
-	struct Halfedge *el;
-	double d, xint, yint;
-	int right_of_site;
-	struct Site *v;
-
-	e1 = el1->ELedge;
-	e2 = el2->ELedge;
-	if (e1 == (struct Edge *)NULL || e2 == (struct Edge *)NULL)
-		return ((struct Site *)NULL);
-	if (e1->reg[1] == e2->reg[1])
-		return ((struct Site *)NULL);
-
-	d = e1->a * e2->b - e1->b * e2->a;
-	/* printf("intersect: d=%g\n", d); */
-	if (-1.0e-20 < d && d < 1.0e-20) {
-		return ((struct Site *)NULL);
-	};
-
-	xint = (e1->c * e2->b - e2->c * e1->b) / d;
-	yint = (e2->c * e1->a - e1->c * e2->a) / d;
-
-	if ((e1->reg[1]->coord.y < e2->reg[1]->coord.y) ||
-			(e1->reg[1]->coord.y == e2->reg[1]->coord.y &&
-			 e1->reg[1]->coord.x < e2->reg[1]->coord.x)) {
-		el = el1;
-		e = e1;
-	} else {
-		el = el2;
-		e = e2;
-	};
-	right_of_site = xint >= e->reg[1]->coord.x;
-	if ((right_of_site && el->ELpm == le) || (!right_of_site && el->ELpm == re))
-		return ((struct Site *)NULL);
-
-	v = (struct Site *)getfree(&sfl);
-	v->refcnt = 0;
-	v->coord.x = xint;
-	v->coord.y = yint;
-	return (v);
-}
-
-/* returns 1 if p is to right of halfedge e */
-int right_of(el, p) struct Halfedge *el;
-struct Point *p;
-{
-	struct Edge *e;
-	struct Site *topsite;
-	int right_of_site, above, fast;
-	double dxp, dyp, dxs, t1, t2, t3, yl;
-
-	e = el->ELedge;
-	topsite = e->reg[1];
-	right_of_site = p->x > topsite->coord.x;
-	if (right_of_site && el->ELpm == le)
-		return (1);
-	if (!right_of_site && el->ELpm == re)
-		return (0);
-
-	if (e->a == 1.0) {
-		dyp = p->y - topsite->coord.y;
-		dxp = p->x - topsite->coord.x;
-		fast = 0;
-		if ((!right_of_site && e->b < 0.0) | (right_of_site && e->b >= 0.0)) {
-			above = dyp >= e->b * dxp;
-			fast = above;
-		} else {
-			above = p->x + p->y * e->b > e->c;
-			if (e->b < 0.0)
-				above = !above;
-			if (!above)
-				fast = 1;
-		};
-		if (!fast) {
-			dxs = topsite->coord.x - (e->reg[0])->coord.x;
-			above = e->b * (dxp * dxp - dyp * dyp) <
-							dxs * dyp * (1.0 + 2.0 * dxp / dxs + e->b * e->b);
-			if (e->b < 0.0)
-				above = !above;
-		};
-	} else /*e->b==1.0 */
-			{
-		yl = e->c - e->a * p->x;
-		t1 = p->y - yl;
-		t2 = p->x - topsite->coord.x;
-		t3 = yl - topsite->coord.y;
-		above = t1 * t1 > t2 * t2 + t3 * t3;
-	};
-	return (el->ELpm == le ? above : !above);
-}
-
-void endpoint(e, lr, s) struct Edge *e;
-int lr;
-struct Site *s;
-{
-	e->ep[lr] = s;
-	ref(s);
-	if (e->ep[re - lr] == (struct Site *)NULL) {
-	} else {
-		out_ep(e);
-		deref(e->reg[le]);
-		deref(e->reg[re]);
-		makefree((struct Freenode *)e, &efl);
-	}
-}
-
-double dist(s, t) struct Site *s, *t;
-{
-	double dx, dy;
-	dx = s->coord.x - t->coord.x;
-	dy = s->coord.y - t->coord.y;
-	return (sqrt(dx * dx + dy * dy));
-}
-
-void makevertex(v) struct Site *v;
-{
-	v->sitenbr = nvertices;
-	nvertices += 1;
-	out_vertex(v);
-}
-
-void deref(v) struct Site *v;
-{
-	v->refcnt -= 1;
-	if (v->refcnt == 0)
-		makefree((struct Freenode *)v, &sfl);
-}
-
-void ref(v) struct Site *v;
-{ v->refcnt += 1; }
diff --git a/src/fortune/heap.c b/src/fortune/heap.c
deleted file mode 100644
index 2ebbd58..0000000
--- a/src/fortune/heap.c
+++ /dev/null
@@ -1,94 +0,0 @@
-#
-#include "defs.h"
-int PQhashsize;
-struct Halfedge *PQhash;
-struct Halfedge *PQfind();
-int PQcount;
-int PQmin;
-int PQempty();
-
-void PQinsert(he, v, offset) struct Halfedge *he;
-struct Site *v;
-double offset;
-{
-	struct Halfedge *last, *next;
-	he->vertex = v;
-	ref(v);
-	he->ystar = v->coord.y + offset;
-	last = &PQhash[PQbucket(he)];
-	while ((next = last->PQnext) != (struct Halfedge *)NULL &&
-				 (he->ystar > next->ystar ||
-					(he->ystar == next->ystar && v->coord.x > next->vertex->coord.x))) {
-		last = next;
-	};
-	he->PQnext = last->PQnext;
-	last->PQnext = he;
-	PQcount += 1;
-}
-
-void PQdelete(he) struct Halfedge *he;
-{
-	struct Halfedge *last;
-
-	if (he->vertex != (struct Site *)NULL) {
-		last = &PQhash[PQbucket(he)];
-		while (last->PQnext != he)
-			last = last->PQnext;
-		last->PQnext = he->PQnext;
-		PQcount -= 1;
-		deref(he->vertex);
-		he->vertex = (struct Site *)NULL;
-	};
-}
-
-int PQbucket(he) struct Halfedge *he;
-{
-	int bucket;
-
-	if (he->ystar < ymin)
-		bucket = 0;
-	else if (he->ystar >= ymax)
-		bucket = PQhashsize - 1;
-	else
-		bucket = (he->ystar - ymin) / deltay * PQhashsize;
-	if (bucket < 0)
-		bucket = 0;
-	if (bucket >= PQhashsize)
-		bucket = PQhashsize - 1;
-	if (bucket < PQmin)
-		PQmin = bucket;
-	return (bucket);
-}
-
-int PQempty() { return (PQcount == 0); }
-
-struct Point PQ_min() {
-	struct Point answer;
-
-	while (PQhash[PQmin].PQnext == (struct Halfedge *)NULL) {
-		PQmin += 1;
-	};
-	answer.x = PQhash[PQmin].PQnext->vertex->coord.x;
-	answer.y = PQhash[PQmin].PQnext->ystar;
-	return (answer);
-}
-
-struct Halfedge *PQextractmin() {
-	struct Halfedge *curr;
-	curr = PQhash[PQmin].PQnext;
-	PQhash[PQmin].PQnext = curr->PQnext;
-	PQcount -= 1;
-	return (curr);
-}
-
-void PQinitialize() {
-	int i;
-//	struct Point *s;
-
-	PQcount = 0;
-	PQmin = 0;
-	PQhashsize = 4 * sqrt_nsites;
-	PQhash = (struct Halfedge *)myalloc(PQhashsize * sizeof *PQhash);
-	for (i = 0; i < PQhashsize; i += 1)
-		PQhash[i].PQnext = (struct Halfedge *)NULL;
-}
diff --git a/src/fortune/main.c b/src/fortune/main.c
deleted file mode 100644
index b6b4476..0000000
--- a/src/fortune/main.c
+++ /dev/null
@@ -1,287 +0,0 @@
-#
-#include <stdio.h>
-#include <stdint.h>
-#include "defs.h"
-#include <math.h>
-struct Site *nextone();
-
-int triangulate, sorted, plot, debug;
-double xmin, xmax, ymin, ymax, deltax, deltay;
-int vert_count, edge_count, line_count, dual_count, site_count;
-double *site_list, *vert_list, *line_list;
-unsigned int *edge_list, *dual_list;
-
-/* sort sites on y, then x, coord */
-int scomp(s1, s2) struct Point *s1, *s2;
-{
-	if (s1->y < s2->y)
-		return (-1);
-	if (s1->y > s2->y)
-		return (1);
-	if (s1->x < s2->x)
-		return (-1);
-	if (s1->x > s2->x)
-		return (1);
-	return (0);
-}
-
-/* read all sites, sort, and compute xmin, xmax, ymin, ymax */
-void readsites(double *lattice) {
-
-	sites = (struct Site *)myalloc(nsites * sizeof *sites);
-	for (unsigned int j = 0; j < nsites; j++) {
-		sites[j].coord.x = lattice[2 * j];
-		sites[j].coord.y = lattice[2 * j + 1];
-		sites[j].sitenbr = j;
-		sites[j].refcnt = 0;
-	}
-	qsort(sites, nsites, sizeof(struct Site), scomp);
-	xmin = sites[0].coord.x;
-	xmax = sites[0].coord.x;
-	for (unsigned int i = 1; i < nsites; i += 1) {
-		if (sites[i].coord.x < xmin)
-			xmin = sites[i].coord.x;
-		if (sites[i].coord.x > xmax)
-			xmax = sites[i].coord.x;
-	};
-	ymin = sites[0].coord.y;
-	ymax = sites[nsites - 1].coord.y;
-}
-
-unsigned int delete_duplicates(unsigned int ne, unsigned int *etv) {
-	unsigned int ndup = 0;
-	bool *duplicates = (bool *)calloc(ne, sizeof(bool));
-	for (unsigned int i = 0; i < ne; i++) {
-		unsigned int v1 = etv[2 * i];
-		unsigned int v2 = etv[2 * i + 1];
-		for (unsigned int j = 0; j < i; j++) {
-			unsigned int w1 = etv[2 * j];
-			unsigned int w2 = etv[2 * j + 1];
-			if (w1 == v1 && w2 == v2) {
-				duplicates[j] = true;
-				ndup++;
-				break;
-			}
-		}
-	}
-	unsigned int newsize = (int)ne - (int)ndup;
-	unsigned int count = 0;
-	for (unsigned int i = 0; i < ne; i++) {
-		if (!duplicates[i]) {
-			etv[2 * count] = etv[2 * i];
-			etv[2 * count + 1] = etv[2 * i + 1];
-			count++;
-		}
-	}
-	free(duplicates);
-	return newsize;
-}
-
-intptr_t *run_voronoi(unsigned int num, double *lattice, bool periodic, double xmin, double xmax, double ymin, double ymax)
-{
-	struct Site *(*next)();
-
-	sorted = 0;
-	triangulate = 0;
-	plot = 0;
-	debug = 0;
-
-	alloclist = (void **)malloc(9 * num * sizeof(void *));
-	allocnum = 0;
-
-	freeinit(&sfl, sizeof *sites);
-
-	unsigned int eff_num = num;
-	double *eff_lattice = lattice;
-
-	if (periodic) {
-		eff_num = 9 * num;
-		eff_lattice = (double *)malloc(2 * eff_num * sizeof(double));
-
-		for (unsigned int i = 0; i < num; i++) {
-			// original sites - our baby boys
-			eff_lattice[2*i] = lattice[2*i];
-			eff_lattice[2*i+1] = lattice[2*i+1];
-
-			// sites to the right
-			eff_lattice[2*(num+i)+1] = lattice[2*i+1] - xmin + xmax;
-			eff_lattice[2*(num+i)] = lattice[2*i];
-
-			// sites to the left
-			eff_lattice[2*(2*num+i)+1] = lattice[2*i+1] - xmax + xmin;
-			eff_lattice[2*(2*num+i)] = lattice[2*i];
-
-			// sites to the top
-			eff_lattice[2*(3*num+i)+1] = lattice[2*i+1];
-			eff_lattice[2*(3*num+i)] = lattice[2*i] - ymin + ymax;
-
-			// sites to the bottom
-			eff_lattice[2*(4*num+i)+1] = lattice[2*i+1];
-			eff_lattice[2*(4*num+i)] = lattice[2*i] - ymax + ymin;
-
-			// sites to the upper right
-			eff_lattice[2*(5*num+i)+1] = lattice[2*i+1] - xmin + xmax;
-			eff_lattice[2*(5*num+i)] = lattice[2*i] - ymin + ymax;
-
-			// sites to the upper left
-			eff_lattice[2*(6*num+i)+1] = lattice[2*i+1] - xmax + xmin;
-			eff_lattice[2*(6*num+i)] = lattice[2*i] - ymin + ymax;
-
-			// sites to the lower left
-			eff_lattice[2*(7*num+i)+1] = lattice[2*i+1] - xmax + xmin;
-			eff_lattice[2*(7*num+i)] = lattice[2*i] + ymin - ymax;
-
-			// sites to the lower right
-			eff_lattice[2*(8*num+i)+1] = lattice[2*i+1] + xmax - xmin;
-			eff_lattice[2*(8*num+i)] = lattice[2*i] + ymin - ymax;
-		}
-	}
-
-	nsites = eff_num;
-	readsites(eff_lattice);
-	if (periodic) free(eff_lattice);
-	next = nextone;
-
-	siteidx = 0;
-	geominit();
-
-	site_list = malloc(2 * nsites * sizeof(double));
-	vert_list = NULL;
-	line_list = NULL;
-	edge_list = NULL;
-	dual_list = NULL;
-	site_count = 0;
-	vert_count = 0;
-	edge_count = 0;
-	line_count = 0;
-	dual_count = 0;
-
-	voronoi(triangulate, next);
-
-	unsigned int real_vert_count = vert_count;
-	unsigned int real_edge_count = edge_count;
-	double *real_vert_list = vert_list;
-	unsigned int *real_edge_list = edge_list;
-	unsigned int *real_dual_list = dual_list;
-
-	if (periodic) {
-		real_vert_count = 0;
-		real_edge_count = 0;
-		real_vert_list = (double *)malloc(2 * vert_count * sizeof(double));
-		real_edge_list = (unsigned int *)malloc(2 * edge_count * sizeof(unsigned int));
-		real_dual_list = (unsigned int *)malloc(3 * dual_count * sizeof(unsigned int));
-		unsigned int *triangle_analyzed = (unsigned int *)malloc(4 * dual_count * sizeof(unsigned int));
-		unsigned int q = 0;
-		int *new_vert_ind = (int *)malloc(vert_count * sizeof(int));
-
-		for (unsigned int i = 0; i < vert_count; i++) {
-			unsigned int t1, t2, t3;
-			t1 = dual_list[3*i]; t2 = dual_list[3*i+1]; t3 = dual_list[3*i+2];
-			if (t1 >= num && t2 >= num && t3 >= num) {
-				new_vert_ind[i] = -1;
-			}
-			else if (t1 < num && t2 < num && t3 < num) {
-				real_vert_list[2*real_vert_count] = vert_list[2*i];
-				real_vert_list[2*real_vert_count+1] = vert_list[2*i+1];
-				real_dual_list[3*real_vert_count] = t1;
-				real_dual_list[3*real_vert_count+1] = t2;
-				real_dual_list[3*real_vert_count+2] = t3;
-				new_vert_ind[i] = real_vert_count;
-				real_vert_count++;
-			}
-			else {
-				unsigned int tt1, tt2, tt3;
-				tt1 = t1 % num; tt2 = t2 % num; tt3 = t3 % num;
-				unsigned int s1, s2, s3;
-				s1 = tt1 < tt2 ? (tt1 < tt3 ? tt1 : tt3) : (tt2 < tt3 ? tt2 : tt3);
-				s3 = tt1 > tt2 ? (tt1 > tt3 ? tt1 : tt3) : (tt2 > tt3 ? tt2 : tt3);
-				s2 = tt1 < tt2 ? (tt1 > tt3 ? tt1 : (tt2 < tt3 ? tt2 : tt3)) : (tt1 < tt3 ? tt1 : (tt2 < tt3 ? tt3: tt2));
-
-				bool matched = false;
-				unsigned int ass_vert;
-
-				for (unsigned int j = 0; j < q; j++) {
-					if (s1 == triangle_analyzed[4*j] && s2 == triangle_analyzed[4*j+1] && s3 == triangle_analyzed[4*j+2]) {
-						matched = true;
-						ass_vert = triangle_analyzed[4*j+3];
-						break;
-					}
-				}
-
-				if (matched) {
-					new_vert_ind[i] = ass_vert;
-				} else {
-					triangle_analyzed[4*q] = s1;
-					triangle_analyzed[4*q+1] = s2;
-					triangle_analyzed[4*q+2] = s3;
-					triangle_analyzed[4*q+3] = real_vert_count;
-					q++;
-					real_vert_list[2*real_vert_count+1] = fmod(2*xmax+vert_list[2*i+1], xmax);
-					real_vert_list[2*real_vert_count] = fmod(2*ymax+vert_list[2*i], ymax);
-					real_dual_list[3*real_vert_count] = t1 % num;
-					real_dual_list[3*real_vert_count+1] = t2 % num;
-					real_dual_list[3*real_vert_count+2] = t3 % num;
-					new_vert_ind[i] = real_vert_count;
-					real_vert_count++;
-				}
-			}
-		}
-		for (unsigned int i = 0; i < edge_count; i++) {
-			unsigned int v1, v2;
-			v1 = edge_list[2 * i];
-			v2 = edge_list[2 * i+1];
-			if (v1 != UINT_MAX && v2 != UINT_MAX) {
-				if (new_vert_ind[v1] >= 0 && new_vert_ind[v2] >=0) {
-					unsigned int nv1 = new_vert_ind[v1];
-					unsigned int nv2 = new_vert_ind[v2];
-					real_edge_list[2*real_edge_count] = nv1 < nv2 ? nv1 : nv2;
-					real_edge_list[2*real_edge_count+1] = nv1 < nv2 ? nv2 : nv1;
-					real_edge_count++;
-				}
-			}
-		}
-		unsigned int new_edge_count = delete_duplicates(real_edge_count, real_edge_list);
-		real_edge_count = new_edge_count;
-		free(triangle_analyzed);
-		free(new_vert_ind);
-		free(dual_list);
-		free(edge_list);
-		free(vert_list);
-	}
-
-
-	intptr_t *output = (intptr_t *)malloc(6 * sizeof(intptr_t));
-	output[0] = (intptr_t)malloc(4 * sizeof(unsigned int));
-	((unsigned int *)output[0])[0] = real_vert_count;
-	((unsigned int *)output[0])[1] = real_edge_count;
-	((unsigned int *)output[0])[2] = line_count;
-	((unsigned int *)output[0])[3] = real_vert_count;
-	output[1] = (intptr_t)site_list;
-	output[2] = (intptr_t)real_vert_list;
-	output[3] = (intptr_t)real_edge_list;
-	output[4] = (intptr_t)line_list;
-	output[5] = (intptr_t)real_dual_list;
-
-	free(ELhash);
-	free(PQhash);
-	free(sites);
-	for (unsigned int i = 0; i < allocnum; i++) {
-		free(alloclist[i]);
-	}
-	free(alloclist);
-
-	return output;
-}
-
-/* return a single in-storage site */
-struct Site *nextone() {
-	for (; siteidx < nsites; siteidx += 1) {
-		if (siteidx == 0 || sites[siteidx].coord.x != sites[siteidx - 1].coord.x ||
-				sites[siteidx].coord.y != sites[siteidx - 1].coord.y) {
-			siteidx += 1;
-			return (&sites[siteidx - 1]);
-		};
-	};
-	return ((struct Site *)NULL);
-}
-
diff --git a/src/fortune/memory.c b/src/fortune/memory.c
deleted file mode 100644
index 3d62a92..0000000
--- a/src/fortune/memory.c
+++ /dev/null
@@ -1,44 +0,0 @@
-#
-#include "defs.h"
-#include <stdio.h>
-
-void freeinit(struct Freelist *fl, int size) {
-	fl->head = (struct Freenode *)NULL;
-	fl->nodesize = size;
-}
-
-char *getfree(fl) struct Freelist *fl;
-{
-	int i;
-	struct Freenode *t;
-	if (fl->head == (struct Freenode *)NULL) {
-		t = (struct Freenode *)myalloc(sqrt_nsites * fl->nodesize);
-		alloclist[allocnum] = (void *)t;
-		allocnum++;
-		for (i = 0; i < sqrt_nsites; i += 1)
-			makefree((struct Freenode *)((char *)t + i * fl->nodesize), fl);
-	};
-	t = fl->head;
-	fl->head = (fl->head)->nextfree;
-	return ((char *)t);
-}
-
-void makefree(curr, fl) struct Freenode *curr;struct Freelist *fl;
-{
-	curr->nextfree = fl->head;
-	fl->head = curr;
-}
-
-int total_alloc;
-char *myalloc(n) unsigned n;
-{
-	char *t;
-	if ((t = malloc(n)) == (char *)0) {
-		fprintf(stderr,
-						"Insufficient memory processing site %d (%d bytes in use)\n",
-						siteidx, total_alloc);
-		exit(1);
-	};
-	total_alloc += n;
-	return (t);
-}
diff --git a/src/fortune/output.c b/src/fortune/output.c
deleted file mode 100644
index d496feb..0000000
--- a/src/fortune/output.c
+++ /dev/null
@@ -1,46 +0,0 @@
-#
-#include "defs.h"
-#include <stdio.h>
-double pxmin, pxmax, pymin, pymax, cradius;
-
-void out_bisector(e) struct Edge *e;
-{
-	if (line_count % nsites == 0) line_list = realloc(line_list, 3 * (nsites + line_count) * sizeof(double));
-	line_list[3*line_count] = e->a;
-	line_list[3*line_count+1] = e->b;
-	line_list[3*line_count+2] = e->c;
-	line_count++;
-}
-
-void out_ep(e) struct Edge *e;
-{
-	if (edge_count % nsites == 0) edge_list = realloc(edge_list, 2 * (nsites + edge_count) * sizeof(unsigned int));
-	edge_list[2 * edge_count] = (e->ep[le] != (struct Site *)NULL ? e->ep[le]->sitenbr : UINT_MAX);
-	edge_list[2 * edge_count + 1] = (e->ep[re] != (struct Site *)NULL ? e->ep[re]->sitenbr : UINT_MAX);
-	edge_count++;
-}
-
-void out_vertex(v) struct Site *v;
-{
-	if (vert_count % nsites == 0) vert_list = realloc(vert_list, 2 * (nsites + vert_count) * sizeof(double));
-	vert_list[2 * vert_count] = v->coord.x;
-	vert_list[2 * vert_count + 1] = v->coord.y;
-	vert_count++;
-}
-
-void out_site(s) struct Site *s;
-{
-	site_list[2 * site_count] = s->coord.x;
-	site_list[2 * site_count + 1] = s->coord.y;
-	site_count++;
-}
-
-void out_triple(s1, s2, s3) struct Site *s1, *s2, *s3;
-{
-	if (dual_count % nsites == 0) dual_list = realloc(dual_list, 3 * (nsites + dual_count) * sizeof(unsigned int));
-	dual_list[dual_count * 3] = s1->sitenbr;
-	dual_list[dual_count * 3 + 1] = s2->sitenbr;
-	dual_list[dual_count * 3 + 2] = s3->sitenbr;
-	dual_count++;
-}
-
diff --git a/src/fortune/voronoi.c b/src/fortune/voronoi.c
deleted file mode 100644
index dc9945f..0000000
--- a/src/fortune/voronoi.c
+++ /dev/null
@@ -1,103 +0,0 @@
-#
-#include "defs.h"
-
-struct Site *sites;
-int nsites;
-int siteidx;
-int sqrt_nsites;
-int nvertices;
-struct Freelist sfl;
-struct Site *bottomsite;
-
-/* implicit parameters: nsites, sqrt_nsites, xmin, xmax, ymin, ymax,
-	 deltax, deltay (can all be estimates).
-	 Performance suffers if they are wrong; better to make nsites,
-	 deltax, and deltay too big than too small.  (?) */
-
-void voronoi(triangulate, nextsite) int triangulate;
-struct Site *(*nextsite)();
-{
-	struct Site *newsite, *bot, *top, *temp, *p;
-	struct Site *v;
-	struct Point newintstar;
-	int pm;
-	struct Halfedge *lbnd, *rbnd, *llbnd, *rrbnd, *bisector;
-	struct Edge *e;
-
-	PQinitialize();
-	bottomsite = (*nextsite)();
-	out_site(bottomsite);
-	ELinitialize();
-
-	newsite = (*nextsite)();
-	while (1) {
-		if (!PQempty())
-			newintstar = PQ_min();
-
-		if (newsite != (struct Site *)NULL &&
-				(PQempty() || newsite->coord.y < newintstar.y ||
-				 (newsite->coord.y == newintstar.y &&
-					newsite->coord.x < newintstar.x))) {/* new site is smallest */
-			out_site(newsite);
-			lbnd = ELleftbnd(&(newsite->coord));
-			rbnd = ELright(lbnd);
-			bot = rightreg(lbnd);
-			e = bisect(bot, newsite);
-			bisector = HEcreate(e, le);
-			ELinsert(lbnd, bisector);
-			if ((p = intersect(lbnd, bisector)) != (struct Site *)NULL) {
-				PQdelete(lbnd);
-				PQinsert(lbnd, p, dist(p, newsite));
-			};
-			lbnd = bisector;
-			bisector = HEcreate(e, re);
-			ELinsert(lbnd, bisector);
-			if ((p = intersect(bisector, rbnd)) != (struct Site *)NULL) {
-				PQinsert(bisector, p, dist(p, newsite));
-			};
-			newsite = (*nextsite)();
-		} else if (!PQempty())
-				/* intersection is smallest */
-				{
-			lbnd = PQextractmin();
-			llbnd = ELleft(lbnd);
-			rbnd = ELright(lbnd);
-			rrbnd = ELright(rbnd);
-			bot = leftreg(lbnd);
-			top = rightreg(rbnd);
-			out_triple(bot, top, rightreg(lbnd));
-			v = lbnd->vertex;
-			makevertex(v);
-			endpoint(lbnd->ELedge, lbnd->ELpm, v);
-			endpoint(rbnd->ELedge, rbnd->ELpm, v);
-			ELdelete(lbnd);
-			PQdelete(rbnd);
-			ELdelete(rbnd);
-			pm = le;
-			if (bot->coord.y > top->coord.y) {
-				temp = bot;
-				bot = top;
-				top = temp;
-				pm = re;
-			}
-			e = bisect(bot, top);
-			bisector = HEcreate(e, pm);
-			ELinsert(llbnd, bisector);
-			endpoint(e, re - pm, v);
-			deref(v);
-			if ((p = intersect(llbnd, bisector)) != (struct Site *)NULL) {
-				PQdelete(llbnd);
-				PQinsert(llbnd, p, dist(p, bot));
-			};
-			if ((p = intersect(bisector, rrbnd)) != (struct Site *)NULL) {
-				PQinsert(bisector, p, dist(p, bot));
-			};
-		} else
-			break;
-	};
-
-	for (lbnd = ELright(ELleftend); lbnd != ELrightend; lbnd = ELright(lbnd)) {
-		e = lbnd->ELedge;
-		out_ep(e);
-	};
-}
diff --git a/src/fracture.c b/src/fracture.c
index 168e519..73059ff 100644
--- a/src/fracture.c
+++ b/src/fracture.c
@@ -103,15 +103,23 @@ int main(int argc, char *argv[]) {
 						lattice_c = 'v';
 						break;
 					case 1:
-						lattice = SQUARE_LATTICE;
-						lattice_c = 's';
+						lattice = DIAGONAL_LATTICE;
+						lattice_c = 'd';
 						break;
 					case 2:
 						lattice = VORONOI_HYPERUNIFORM_LATTICE;
 						lattice_c = 'h';
 						break;
+					case 3:
+						lattice = TRIANGULAR_LATTICE;
+						lattice_c = 't';
+						break;
+          case 4:
+            lattice = SQUARE_LATTICE;
+            lattice_c = 's';
+            break;
 					default:
-						printf("lattice specifier must be 0 (VORONOI_LATTICE), 1 (SQUARE_LATTICE), or 2 (VORONOI_HYPERUNIFORM_LATTICE).\n");
+						printf("lattice specifier must be 0 (VORONOI_LATTICE), 1 (DIAGONAL_LATTICE), or 2 (VORONOI_HYPERUNIFORM_LATTICE).\n");
 						exit(EXIT_FAILURE);
 				}
 				break;
@@ -270,7 +278,7 @@ int main(int argc, char *argv[]) {
 	for (uint32_t i = 0; i < N; i++) {
 		printf("\033[F\033[JFRACTURE: %0*d / %d\n", (uint8_t)log10(N) + 1, i + 1, N);
 
-		graph_t *g = graph_create(lattice, boundary, L, use_dual, &c);
+		graph_t *g = graph_create(lattice, boundary, L, use_dual);
 		net_t *net = net_create(g, inf, beta, crack_len, use_voltage_boundaries, &c);
 		net_t *tmp_net = net_copy(net, &c);
 		data_t *data = net_fracture(tmp_net, &c, cutoff);
@@ -406,7 +414,7 @@ int main(int argc, char *argv[]) {
 		}
 
 		if (save_cluster_dist) {
-			uint_t *tmp_cluster_dist = get_cluster_dist(net, &c);
+			uint_t *tmp_cluster_dist = get_cluster_dist(net);
 			for (uint_t j = 0; j < g->dnv; j++) {
 				cluster_size_dist[j] += tmp_cluster_dist[j];
 			}
@@ -415,7 +423,7 @@ int main(int argc, char *argv[]) {
 
 
 		net_free(net, &c);
-		graph_free(g, &c);
+		graph_free(g);
 	}
 
 	printf("\033[F\033[JFRACTURE: COMPLETE\n");
diff --git a/src/fracture.h b/src/fracture.h
index 0a3a687..b1114fb 100644
--- a/src/fracture.h
+++ b/src/fracture.h
@@ -23,6 +23,10 @@
 #include <sys/types.h>
 #include <unistd.h>
 
+#include <jst/graph.h>
+#include <jst/rand.h>
+
+
 // these defs allow me to switch to long int cholmod in a sitch
 #define int_t int
 #define uint_t unsigned int
@@ -31,54 +35,6 @@
 
 #define GSL_RAND_GEN gsl_rng_mt19937
 
-typedef enum lattice_t {
-	VORONOI_LATTICE,
-	SQUARE_LATTICE,
-	VORONOI_HYPERUNIFORM_LATTICE
-} lattice_t;
-
-typedef enum bound_t {
-	FREE_BOUND,
-	CYLINDER_BOUND,
-	TORUS_BOUND,
-	EMBEDDED_BOUND
-} bound_t;
-
-typedef struct {
-	uint_t ne;
-	uint_t nv;
-	uint_t dnv;
-	uint_t *ev;
-	uint_t *dev;
-	double *vx;
-	double *dvx;
-} frame_t;
-
-typedef struct {
-	uint_t L;
-	bound_t boundary;
-	uint_t ne;
-	uint_t nv;
-	uint_t dnv;
-	uint_t nb;
-	uint_t *ev; 
-	uint_t *dev;
-	double *vx;
-	double *dvx;
-	uint_t *vei;
-	uint_t *ve;
-	uint_t *dvei;
-	uint_t *dve;
-	uint_t *bi;
-	uint_t *b;
-	uint_t *nbi;
-	uint_t *bni;
-	bool *bq;
-	uint_t *spanning_edges;
-	uint_t num_spanning_edges;
-	cholmod_sparse *voltcurmat;
-} graph_t;
-
 typedef struct {
 	const graph_t *graph;
 	bool *fuses;
@@ -91,6 +47,7 @@ typedef struct {
 	uint_t dim;
 	uint_t nep;
 	uint_t *evp;
+	cholmod_sparse *voltcurmat;
 } net_t;
 
 typedef struct {
@@ -102,11 +59,6 @@ typedef struct {
 
 intptr_t *run_voronoi(uint_t num_coords, double *coords, bool periodic, double xmin, double xmax, double ymin, double ymax);
 
-int update_components(const cholmod_sparse *laplacian, uint_t *marks,
-											int old_num_components, int v1, int v2, int exclude);
-
-uint_t *find_components(const cholmod_sparse *laplacian, uint_t skip);
-
 cholmod_sparse *gen_adjacency(const net_t *net, bool dual, bool use_gp, bool symmetric, cholmod_common *c);
 
 cholmod_sparse *gen_laplacian(const net_t *net, cholmod_common *c);
@@ -121,6 +73,7 @@ double dual_vert_to_coord(uint_t width, bool periodic, uint_t vert,
 													bool index);
 
 void factor_update(cholmod_factor *factor, uint_t v1, uint_t v2, cholmod_common *c);
+void factor_update2(cholmod_factor *factor, uint_t v1, cholmod_common *c);
 
 void net_notch(net_t *net, double notch_len, cholmod_common *c);
 data_t *net_fracture(net_t *net, cholmod_common *c, double cutoff);
@@ -142,35 +95,19 @@ cholmod_sparse *gen_voltcurmat(uint_t num_edges, uint_t num_verts,
 
 net_t *net_copy(const net_t *net, cholmod_common *c);
 
-graph_t *ini_square_network(uint_t width, bound_t boundary, bool side_bounds,
-												 cholmod_common *c);
-
-void graph_free(graph_t *network, cholmod_common *c);
 void net_free(net_t *instance, cholmod_common *c);
 
 net_t *net_create(const graph_t *g, double inf, double beta, double notch_len, bool vb, cholmod_common *c);
 
-graph_t *ini_voro_graph(uint_t L, bound_t boundary, bool use_dual,
-													double *(*genfunc)(uint_t, bound_t, gsl_rng *, uint_t *),
-													cholmod_common *c);
-
 bool break_edge(net_t *instance, uint_t edge, cholmod_common *c);
 
-void finish_instance(net_t *instance, cholmod_common *c);
-
-net_t *coursegrain_square(net_t *instance, graph_t *network_p, cholmod_common *c);
-
-uint_t *get_clusters(net_t *instance, cholmod_common *c);
+components_t *get_clusters(net_t *instance);
 
-uint_t *get_cluster_dist(net_t *instance, cholmod_common *c);
+uint_t *get_cluster_dist(net_t *instance);
 
-double *genfunc_uniform(uint_t num, gsl_rng *r);
-double *genfunc_hyperuniform(uint_t num, gsl_rng *r);
 void randfunc_flat(gsl_rng *r, double *x, double *y);
 void randfunc_gaus(gsl_rng *r, double *x, double *y);
 
-uint_t **get_dists(const graph_t *network);
-uint_t *dijkstra(const graph_t *g, uint_t source);
 double *get_corr(net_t *instance, uint_t **dists, cholmod_common *c);
 
 double *bin_values(graph_t *network, uint_t width, double *values);
@@ -181,18 +118,6 @@ data_t *data_create(uint_t num_edges);
 void data_free(data_t *data);
 void data_update(data_t *data, uint_t last_broke, long double strength, double conductivity);
 
-graph_t *graph_create(lattice_t lattice, bound_t bound, uint_t L, bool dual, cholmod_common *c);
-
-uint_t find_cycles(uint_t num_edges, const bool *fuses, const uint_t *ev, const uint_t *vei, const uint_t *ve, int **cycles);
-
-bool set_connected(const cholmod_sparse *laplacian, uint_t *marks, int vertex, int label, int stop_at, int exclude);
-
-unsigned long int rand_seed();
-
 long double rand_dist_pow(const gsl_rng *r, double beta);
 
-double *spheres(int N, double bidispersityratio, double bidispersityfraction, double maxpf, double maxpressure, double maxcollisionrate);
-
-frame_t *frame_create(lattice_t lattice, uint_t L, bool dual);
-void frame_free(frame_t *frame);
 bool is_in(uint_t len, uint_t *list, uint_t element);
diff --git a/src/frame_create.c b/src/frame_create.c
deleted file mode 100644
index 89ce69d..0000000
--- a/src/frame_create.c
+++ /dev/null
@@ -1,167 +0,0 @@
-
-#include "fracture.h"
-
-uint_t *get_voro_dual_edges(uint_t num_edges,
-																	uint_t num_verts, uint_t *edges,
-																	uint_t *triangles) {
-	uint_t *dual_edges =
-			(uint_t *)malloc(2 * num_edges * sizeof(uint_t));
-	uint_t place = 0;
-	for (uint_t i = 0; i < num_edges; i++) {
-		uint_t v1, v2;
-		v1 = edges[2 * i];
-		v2 = edges[2 * i + 1];
-		if (v1 < num_verts && v2 < num_verts) {
-			bool found_match = false;
-			for (uint_t j = 0; j < 3; j++) {
-				for (uint_t k = 0; k < 3; k++) {
-					uint_t t11, t12, t21, t22;
-					t11 = triangles[3 * v1 + j];
-					t12 = triangles[3 * v1 + ((j + 1) % 3)];
-					t21 = triangles[3 * v2 + k];
-					t22 = triangles[3 * v2 + ((k + 1) % 3)];
-					if ((t11 == t21 && t12 == t22) || (t11 == t22 && t12 == t21)) {
-						dual_edges[2 * place] = t11 < t12 ? t11 : t12;
-						dual_edges[2 * place + 1] = t11 < t12 ? t12 : t11;
-						place++;
-						found_match = true;
-						break;
-					}
-				}
-				if (found_match)
-					break;
-			}
-		}
-	}
-
-	return dual_edges;
-}
-
-frame_t *frame_create_voronoi(uint_t L, bool dual, bool hyperuniform) {
-	double *dvx = NULL;
-	uint_t dnv = 2 * pow(L / 2, 2);
-
-	{
-		gsl_rng *r = gsl_rng_alloc(gsl_rng_mt19937);
-		gsl_rng_set(r, rand_seed());
-
-		if (hyperuniform) {
-			dvx = genfunc_hyperuniform(dnv, r);
-		} else {
-			dvx = genfunc_uniform(dnv, r);
-		}
-
-		gsl_rng_free(r);
-	}
-
-	// retrieve a periodic voronoi tesselation of the lattice
-	intptr_t *vout = run_voronoi(dnv, dvx, true, 0, 1, 0, 1);
-
-	uint_t nv = ((uint_t *)vout[0])[0];
-	uint_t ne = ((uint_t *)vout[0])[1];
-	double *vx = (double *)vout[2];
-	uint_t *ev = (uint_t *)vout[3];
-	uint_t *voro_tris = (uint_t *)vout[5];
-
-	free((void *)vout[0]);
-	free((void *)vout[1]);
-	free((void *)vout[4]);
-	free(vout);
-
-	// get dual edges of the fully periodic graph
-	uint_t *dev = get_voro_dual_edges(ne, nv, ev, voro_tris);
-
-	frame_t *frame = (frame_t *)malloc(sizeof(frame_t));
-	frame->ne = ne;
-
-	// when use_dual is specificed, the edge and vertex sets are swapped with the
-	// dual edge and dual vertex sets.  once formally relabelled, everything
-	// works the same way
-	if (dual) {
-		frame->nv = dnv;
-		frame->dnv = nv;
-		frame->ev = dev;
-		frame->dev = ev;
-		frame->vx = dvx;
-		frame->dvx = vx;
-	} else {
-		frame->nv = nv;
-		frame->dnv = dnv;
-		frame->ev = ev;
-		frame->dev = dev;
-		frame->vx = vx;
-		frame->dvx = dvx;
-	}
-
-	return frame;
-}
-
-frame_t *frame_create_square(uint_t L, bool dual) {
-	uint_t nv = 2 * pow(L / 2, 2);
-	uint_t ne = pow(L, 2);
-
-	uint_t *ev = (uint_t *)malloc(2 * ne * sizeof(uint_t));
-	uint_t *dev = (uint_t *)malloc(2 * ne * sizeof(uint_t));
-	double *vx = (double *)malloc(2 * nv * sizeof(double));
-	double *dvx = (double *)malloc(2 * nv * sizeof(double));
-
-	for (uint_t i = 0; i < ne; i++) {
-		uint_t x = i / L;
-		uint_t y = i % L;
-
-		ev[2 * i] = (L * x) / 2 + ((y + x % 2) / 2) % (L / 2);
-		ev[2 * i + 1] = ((L * (x + 1)) / 2 + ((y + (x + 1) % 2) / 2) % (L / 2)) % nv;
-
-		dev[2 * i] = (L * x) / 2 + ((y + (x + 1) % 2) / 2) % (L / 2);
-		dev[2 * i + 1] = ((L * (x + 1)) / 2 + ((y + x % 2) / 2) % (L / 2)) % nv;
-	}
-
-	double dx = 1. / L;
-
-	for (uint_t i = 0; i < nv; i++) {
-		vx[2 * i] = dx * ((1 + i / (L / 2)) % 2 + 2 * (i % (L / 2)));
-		vx[2 * i + 1] = dx * (i / (L / 2));
-
-		dvx[2 * i] = dx * ((i / (L / 2)) % 2 + 2 * (i % (L / 2)));
-		dvx[2 * i + 1] = dx * (i / (L / 2));
-	}
-
-	frame_t *frame = (frame_t *)malloc(sizeof(frame_t));
-	frame->ne = ne;
-	frame->nv = nv;
-	frame->dnv = nv;
-
-	if (dual) {
-		frame->ev = dev;
-		frame->dev = ev;
-		frame->vx = dvx;
-		frame->dvx = vx;
-	} else {
-		frame->ev = ev;
-		frame->dev = dev;
-		frame->vx = vx;
-		frame->dvx = dvx;
-	}
-
-	return frame;
-}
-
-frame_t *frame_create(lattice_t lattice, uint_t L, bool dual) {
-	switch (lattice) {
-		case (SQUARE_LATTICE):
-			return frame_create_square(L, dual);
-		case (VORONOI_LATTICE):
-			return frame_create_voronoi(L, dual, false);
-		case (VORONOI_HYPERUNIFORM_LATTICE):
-			return frame_create_voronoi(L, dual, true);
-	}
-}
-
-void frame_free(frame_t *frame) {
-	free(frame->ev);
-	free(frame->dev);
-	free(frame->vx);
-	free(frame->dvx);
-	free(frame);
-}
-
diff --git a/src/get_dual_clusters.c b/src/get_dual_clusters.c
deleted file mode 100644
index 6090fb8..0000000
--- a/src/get_dual_clusters.c
+++ /dev/null
@@ -1,36 +0,0 @@
-
-#include "fracture.h"
-
-unsigned int *get_clusters(net_t *instance, cholmod_common *c) {
-	cholmod_sparse *s_dual = gen_adjacency(instance, true, false, false, c);
-
-	unsigned int *dual_marks = find_components(s_dual, 0);
-	CHOL_F(free_sparse)(&s_dual, c);
-
-	return dual_marks;
-}
-
-unsigned int *get_cluster_dist(net_t *instance, cholmod_common *c) {
-	unsigned int *clusters = get_clusters(instance, c);
-	unsigned int *cluster_dist = (unsigned int *)calloc(
-			instance->graph->dnv, sizeof(unsigned int));
-
-	unsigned int cur_mark = 0;
-	while (true) {
-		cur_mark++;
-		unsigned int num_in_cluster = 0;
-		for (unsigned int i = 0; i < instance->graph->dnv; i++) {
-			if (clusters[i] == cur_mark)
-				num_in_cluster++;
-		}
-
-		if (num_in_cluster == 0)
-			break;
-
-		cluster_dist[num_in_cluster - 1]++;
-	}
-
-	free(clusters);
-
-	return cluster_dist;
-}
diff --git a/src/graph_components.c b/src/graph_components.c
deleted file mode 100644
index 9680675..0000000
--- a/src/graph_components.c
+++ /dev/null
@@ -1,185 +0,0 @@
-
-#include "fracture.h"
-
-bool set_connected(const cholmod_sparse *laplacian, uint_t *marks,
-									 int vertex, int label, int stop_at, int exclude) {
-	unsigned int num_verts = (int_t)laplacian->nrow;
-
-	int_t *ia = (int_t *)laplacian->p;
-	int_t *ja = (int_t *)laplacian->i;
-	double *a = (double *)laplacian->x;
-
-	bool stopped = false;
-
-	int *queue = (int *)malloc((num_verts) * sizeof(int));
-	assert(queue != NULL);
-
-	int queue_pos = 0;
-
-	int *component_list = (int *)malloc((num_verts) * sizeof(int));
-	assert(component_list != NULL);
-
-	int list_pos = 0;
-	queue[0] = vertex;
-	component_list[0] = vertex;
-
-	unsigned int old_label = marks[vertex];
-	marks[vertex] = label;
-
-	while (queue_pos >= 0) {
-		int next_vertex = queue[queue_pos];
-		queue_pos--;
-		for (int j = 0; j < ia[next_vertex + 1] - ia[next_vertex]; j++) {
-			if (ja[ia[next_vertex] + j] == stop_at && a[ia[next_vertex] + j] != 0) {
-				// if we run into the other vertex, the components haven't changed
-				stopped = true; queue_pos = -1;
-				break;
-			}
-			if (marks[ja[ia[next_vertex] + j]] != label &&
-					a[ia[next_vertex] + j] != 0 &&
-					ja[ia[next_vertex] + j] < num_verts - exclude) {
-				marks[ja[ia[next_vertex] + j]] = label;
-				queue_pos++;
-				queue[queue_pos] = ja[ia[next_vertex] + j];
-				list_pos++;
-				component_list[list_pos] = ja[ia[next_vertex] + j];
-			}
-		}
-	}
-
-	if (stopped) {
-		for (unsigned int i = 0; i <= list_pos; i++) {
-			marks[component_list[i]] = old_label;
-		}
-	}
-
-	free(queue);
-	free(component_list);
-
-	if (stopped)
-		return false;
-	else
-		return true;
-}
-
-int update_components(const cholmod_sparse *laplacian, unsigned int *marks,
-											int old_num_components, int v1, int v2, int exclude) {
-	assert(laplacian != NULL);
-	assert(marks != NULL);
-
-	if (set_connected(laplacian, marks, v1, old_num_components + 1, v2,
-										exclude)) {
-		return old_num_components + 1;
-	} else
-		return old_num_components;
-}
-
-unsigned int *find_components(const cholmod_sparse *laplacian, unsigned int skip) {
-	size_t num_verts = laplacian->nrow;
-	unsigned int *marks = (unsigned int *)calloc(num_verts, sizeof(unsigned int));
-
-	int num_components = 0;
-
-	for (int i = 0; i < num_verts; i++) {
-		if (marks[i] == 0) {
-			num_components++;
-			set_connected(laplacian, marks, i, num_components, -1, skip);
-		}
-	}
-
-	return marks;
-}
-
-uint_t find_cycles(uint_t num_edges, const bool *fuses, const uint_t *ev, const unsigned
-		int *vei, const uint_t *ve, int **cycles) {
-	uint_t num_cycles = 0;
-	uint_t *elist = (uint_t *)malloc(num_edges * sizeof(uint_t));
-	uint_t *side = (uint_t *)calloc(num_edges, sizeof(uint_t));
-	uint_t *num = (uint_t *)malloc(num_edges * sizeof(uint_t));
-	for (uint_t i = 0; i < num_edges; i++) {
-		if (fuses[i]) {
-		bool in_cycle = false;
-		for (uint_t j = 0; j < num_cycles; j++) {
-			uint_t k = 0;
-			int e;
-			while ((e = cycles[j][k]) >= 0) {
-				if (e == i) {
-					in_cycle = true;
-					break;
-				}
-				k++;
-			}
-			if (in_cycle) {
-				break;
-			}
-		}
-		if (!in_cycle) {
-			uint_t pos = 0;
-			uint_t cur_e = i;
-			bool *included = (bool *)calloc(num_edges, sizeof(bool));
-			included[cur_e] = true;
-			elist[0] = cur_e;
-			side[0] = 1;
-			num[0] = 0;
-			while (true) {
-				uint_t cv = ev[2 * cur_e + side[pos]];
-				uint_t new_e = cur_e;
-				uint_t j;
-				for (j = num[pos]; j < vei[cv+1] - vei[cv]; j++) {
-					new_e = ve[vei[cv] + j];
-					if (new_e != cur_e && fuses[new_e]) break;
-				}
-				if (new_e != cur_e && fuses[new_e]) {
-					if (new_e == elist[0] && cv == ev[2 * elist[0] + !side[0]]) {
-						pos++;
-						cycles[2*num_cycles] = (int *)malloc((pos + 1) * sizeof(int));
-						cycles[2*num_cycles+1] = (int *)malloc((pos + 1) * sizeof(int));
-						for (uint_t i = 0; i < pos; i++) {
-							cycles[2*num_cycles][i] = elist[i];
-							cycles[2*num_cycles+1][i] = side[i];
-						}
-						cycles[2*num_cycles][pos] = -1;
-						cycles[2*num_cycles+1][pos] = -1;
-						num_cycles++;
-						pos--;
-						num[pos]++;
-						included[pos] = false;
-						cur_e = elist[pos];
-					} else if (included[new_e]) {
-						if (pos == 0) break;
-						included[cur_e] = false;
-						pos--;
-						num[pos]++;
-						cur_e = elist[pos];
-					} else {
-						num[pos] = j;
-						pos++;
-						elist[pos] = new_e;
-						included[new_e] = true;
-						uint_t nv1 = ev[2 * new_e];
-						uint_t nv2 = ev[2 * new_e + 1];
-						uint_t v = nv1 == cv ? nv2 : nv1;
-						side[pos] = v == nv1 ? 0 : 1;
-						num[pos] = 0;
-						cur_e = new_e;
-					}
-				} else {
-					if (pos == 0) break;
-					included[cur_e] = false;
-					pos--;
-					num[pos]++;
-					cur_e = elist[pos];
-				}
-			}
-			free(included);
-		}
-		}
-	}
-
-	free(elist);
-	free(side);
-	free(num);
-
-	return num_cycles;
-}
-
diff --git a/src/graph_create.c b/src/graph_create.c
deleted file mode 100644
index 09a3aed..0000000
--- a/src/graph_create.c
+++ /dev/null
@@ -1,299 +0,0 @@
-
-#include "fracture.h"
-
-uint_t *get_spanning_edges(uint_t num_edges, uint_t *edges_to_verts, double *vert_coords, double cut, uint_t *n) {
-	uint_t *spanning_edges = (uint_t *)malloc(num_edges * sizeof(uint_t));
-	(*n) = 0;
-	for (uint_t i = 0; i < num_edges; i++) {
-		uint_t v1, v2;
-		v1 = edges_to_verts[2 * i];
-		v2 = edges_to_verts[2 * i + 1];
-		double v1y, v2y;
-		v1y = vert_coords[2 * v1 + 1];
-		v2y = vert_coords[2 * v2 + 1];
-		if ((fabs(v1y - v2y) < 0.5) && ((v1y <= cut && v2y > cut) || (v1y >= cut && v2y < cut))) {
-			spanning_edges[*n] = i;
-			(*n)++;
-		}
-	}
-	return spanning_edges;
-}
-
-double *get_edge_coords(uint_t num_edges, double *vert_coords,
-												uint_t *edges_to_verts) {
-	double *output = (double *)malloc(2 * num_edges * sizeof(double));
-
-	for (uint_t i = 0; i < num_edges; i++) {
-		uint_t v1, v2;
-		double v1x, v1y, v2x, v2y, dx, dy;
-		v1 = edges_to_verts[2 * i];
-		v2 = edges_to_verts[2 * i + 1];
-		output[2 * i] = 0;
-		output[2 * i + 1] = 0;
-		v1x = vert_coords[2 * v1];
-		v1y = vert_coords[2 * v1 + 1];
-		v2x = vert_coords[2 * v2];
-		v2y = vert_coords[2 * v2 + 1];
-		dx = v1x - v2x;
-		dy = v1y - v2y;
-		if (fabs(dx) > 0.5) {
-			if (dx > 0) {
-				v2x = v2x + 1;
-			} else {
-				v1x = v1x + 1;
-			}
-		}
-		if (fabs(dy) > 0.5) {
-			if (dy > 0) {
-				v2y = v2y + 1;
-			} else {
-				v1y = v1y + 1;
-			}
-		}
-		output[2 * i] = (v1x + v2x) / 2;
-		output[2 * i + 1] = (v1y + v2y) / 2;
-	}
-
-	return output;
-}
-
-uint_t *get_verts_to_edges_ind(uint_t num_verts,
-																		 uint_t num_edges,
-																		 const uint_t *edges_to_verts) {
-	uint_t *output =
-			(uint_t *)calloc(num_verts + 1, sizeof(uint_t));
-	assert(output != NULL);
-
-	for (uint_t i = 0; i < 2 * num_edges; i++) {
-		if (edges_to_verts[i] < num_verts) {
-			output[edges_to_verts[i] + 1]++;
-		}
-	}
-
-	for (uint_t i = 0; i < num_verts; i++) {
-		output[i + 1] += output[i];
-	}
-
-	return output;
-}
-
-uint_t *get_verts_to_edges(uint_t num_verts, uint_t num_edges,
-																 const uint_t *edges_to_verts,
-																 const uint_t *verts_to_edges_ind) {
-	uint_t *output = (uint_t *)calloc(verts_to_edges_ind[num_verts],
-																								sizeof(uint_t));
-	uint_t *counts =
-			(uint_t *)calloc(num_verts, sizeof(uint_t));
-	for (int i = 0; i < 2 * num_edges; i++) {
-		if (edges_to_verts[i] < num_verts) {
-			output[verts_to_edges_ind[edges_to_verts[i]] +
-						 counts[edges_to_verts[i]]] = i / 2;
-			counts[edges_to_verts[i]]++;
-		}
-	}
-
-	free(counts);
-
-	return output;
-}
-
-uint_t get_cut_edges(uint_t ne, const uint_t *ev, const double *vx, bool both, uint_t *ce) {
-	uint_t nce = 0;
-
-	for (uint_t i = 0; i < ne; i++) {
-		uint_t v1 = ev[2 * i];
-		uint_t v2 = ev[2 * i + 1];
-
-		double v1y = vx[2 * v1 + 1];
-		double v2y = vx[2 * v2 + 1];
-
-		if (fabs(v1y - v2y) > 0.5) {
-			ce[nce] = i;
-			nce++;
-		} else if (both) {
-			double v1x = vx[2 * v1];
-			double v2x = vx[2 * v2];
-
-			if (fabs(v1x - v2x) > 0.5) {
-				ce[nce] = i;
-				nce++;
-			}
-		}
-	}
-
-	return nce;
-}
-
-graph_t *graph_create(lattice_t lattice, bound_t bound, uint_t L, bool dual, cholmod_common *c) {
-	graph_t *g = (graph_t *)calloc(1, sizeof(graph_t));
-	frame_t *f = frame_create(lattice, L, dual);
-
-	g->L = L;
-	g->boundary = bound;
-	g->ne = f->ne;
-
-	if (bound == TORUS_BOUND) {
-		g->nv = f->nv;
-		g->dnv = f->dnv;
-		g->nb = 1;
-
-		g->ev = f->ev;
-		f->ev = NULL;
-		g->dev = f->dev;
-		f->dev = NULL;
-		g->vx = f->vx;
-		f->vx = NULL;
-		g->dvx = f->dvx;
-		f->dvx = NULL;
-
-		// the boundary for the torus consists of a list of edges required to cut
-		// the torus into a cylinder
-		g->bi = (uint_t *)calloc(2, sizeof(uint_t));
-		g->b = (uint_t *)malloc(g->ne * sizeof(uint_t));
-		g->bi[1] = get_cut_edges(g->ne, g->ev, g->vx, false, g->b);
-		g->bq = (bool *)calloc(g->ne, sizeof(bool));
-		for (uint_t i = 0; i < g->bi[1]; i++) {
-			g->bq[g->b[i]] = true;
-		}
-	} else {
-		uint_t *ce = (uint_t *)malloc(g->ne * sizeof(uint_t));
-		uint_t nce = 0;
-
-		if (bound == CYLINDER_BOUND) {
-			g->nb = 2;
-			nce = get_cut_edges(f->ne, f->ev, f->vx, false, ce);
-		} else {
-			g->nb = 4;
-			nce = get_cut_edges(f->ne, f->ev, f->vx, true, ce);
-		}
-
-		g->nv = f->nv;
-		g->dnv = f->dnv;
-		g->vx = (double *)malloc(2 * (f->nv + nce) * sizeof(double));
-		g->dvx = (double *)malloc(2 * (f->dnv + nce) * sizeof(double));
-		g->ev = f->ev;
-		g->dev = f->dev;
-		f->ev = NULL;
-		f->dev = NULL;
-		memcpy(g->vx, f->vx, 2 * f->nv * sizeof(double));
-		memcpy(g->dvx, f->dvx, 2 * f->dnv * sizeof(double));
-
-		uint_t nbv = 0;
-		uint_t *bv = (uint_t *)calloc(f->nv, sizeof(uint_t));
-		uint_t *dbv = (uint_t *)calloc(f->dnv, sizeof(uint_t));
-		uint_t nside = 0;
-		bool *side = (bool *)calloc(f->nv, sizeof(bool));
-
-		for (uint_t i = 0; i < nce; i++) {
-			uint_t cv1 = g->ev[2 * ce[i]];
-			uint_t cv2 = g->ev[2 * ce[i] + 1];
-			uint_t dv1 = g->dev[2 * ce[i]];
-			uint_t dv2 = g->dev[2 * ce[i] + 1];
-
-			uint_t cin = 1;
-
-			if (bound == FREE_BOUND && (f->vx[2 * cv2] - f->vx[2 * cv1]) > 0.5) {
-				cin = 0; 
-			}
-
-			uint_t vin = f->vx[2 * cv1 + cin] < f->vx[2 * cv2 + cin] ? 0 : 1;
-			uint_t dvin = f->dvx[2 * dv1 + cin] < f->dvx[2 * dv2 + cin] ? 0 : 1;
-
-			if (bv[g->ev[2 * ce[i] + vin]] == 0) {
-				nbv++;
-				if (cin == 0) {
-					nside++;
-					side[g->ev[2 * ce[i] + vin]] = true;
-				}
-
-				bv[g->ev[2 * ce[i] + vin]] = g->nv;
-
-				g->vx[2 * g->nv + cin] = 1 + f->vx[2 * g->ev[2 * ce[i] + vin] + cin];
-				g->vx[2 * g->nv + !cin] = f->vx[2 * g->ev[2 * ce[i] + vin] + !cin];
-				g->ev[2 * ce[i] + vin] = g->nv;
-
-				g->nv++;
-			} else {
-				g->ev[2 * ce[i] + vin] = bv[g->ev[2 * ce[i] + vin]];
-			}
-			if (dbv[g->dev[2 * ce[i] + dvin]] == 0) {
-				dbv[g->dev[2 * ce[i] + dvin]] = g->dnv;
-
-				if (f->dvx[2 * g->dev[2 * ce[i] + dvin] + cin] < 0.5) {
-					g->dvx[2 * g->dnv + cin] = 1 + f->dvx[2 * g->dev[2 * ce[i] + dvin] + cin];
-				} else {
-					g->dvx[2 * g->dnv + cin] = f->dvx[2 * g->dev[2 * ce[i] + dvin] + cin];
-				}
-				g->dvx[2 * g->dnv + !cin] = f->dvx[2 * g->dev[2 * ce[i] + dvin] + !cin];
-				g->dev[2 * ce[i] + dvin] = g->dnv;
-
-				g->dnv++;
-			} else {
-				g->dev[2 * ce[i] + dvin] = dbv[g->dev[2 * ce[i] + dvin]];
-			}
-		}
-
-		g->bi = (uint_t *)calloc(1 + g->nb, sizeof(uint_t));
-		g->b = (uint_t *)malloc(2 * nbv * sizeof(uint_t));
-
-		g->bi[1] = ((int_t)nbv - (int_t)nside);
-		g->bi[g->nb] = 2 * nbv;
-
-		if (bound == FREE_BOUND) {
-			g->bi[2] = 2 * ((int_t)nbv - (int_t)nside);
-			g->bi[3] = 2 * (int_t)nbv - (int_t)nside;
-		}
-
-		uint_t n_ins0 = 0;
-		uint_t n_ins1 = 0;
-
-		g->nbi = (uint_t *)malloc(((int_t)g->nv - (int_t)g->bi[g->nb]) * sizeof(uint_t));
-		g->bni = (uint_t *)malloc((g->nv + 1) * sizeof(uint_t));
-		g->bq = (bool *)calloc(g->nv, sizeof(bool));
-		uint_t n_tmp = 0;
-
-		for (uint_t i = 0; i < f->nv; i++) {
-			g->bni[i] = n_tmp;
-			if (bv[i] != 0) {
-				g->bq[i] = true;
-				g->bq[bv[i]] = true;
-				if (side[i]) {
-					g->b[g->bi[2] + n_ins1] = i;
-					g->b[g->bi[3] + n_ins1] = bv[i];
-					n_ins1++;
-				} else {
-					g->b[g->bi[0] + n_ins0] = i;
-					g->b[g->bi[1] + n_ins0] = bv[i];
-					n_ins0++;
-				}
-			} else {
-				g->nbi[n_tmp] = i;
-				n_tmp++;
-			}
-		}
-
-		for (uint_t i = 0; i < g->nv - f->nv + 1; i++) {
-			g->bni[f->nv + i] = n_tmp;
-		}
-
-		free(bv);
-		free(dbv);
-		free(side);
-	}
-
-	g->vei = get_verts_to_edges_ind(g->nv, g->ne, g->ev);
-	g->ve = get_verts_to_edges(g->nv, g->ne, g->ev, g->vei);
-	g->dvei = get_verts_to_edges_ind(g->dnv, g->ne, g->dev);
-	g->dve = get_verts_to_edges(g->dnv, g->ne, g->dev, g->dvei);
-
-	g->voltcurmat = gen_voltcurmat(g->ne, g->nv, g->ev, c);
-	uint_t num_spanning_edges;
-	g->spanning_edges = get_spanning_edges(g->ne, g->ev, g->vx, 0.5, &num_spanning_edges);
-	g->num_spanning_edges = num_spanning_edges;
-
-	frame_free(f);
-
-	return g;
-}
-
-
diff --git a/src/graph_free.c b/src/graph_free.c
deleted file mode 100644
index ee30c99..0000000
--- a/src/graph_free.c
+++ /dev/null
@@ -1,19 +0,0 @@
-
-#include "fracture.h"
-
-void graph_free(graph_t *g, cholmod_common *c) {
-	free(g->ev);
-	free(g->vei);
-	free(g->ve);
-	free(g->bi);
-	free(g->b);
-	free(g->vx);
-	free(g->dvx);
-	free(g->dev);
-	free(g->dvei);
-	free(g->dve);
-	free(g->nbi);
-	free(g->bq);
-	CHOL_F(free_sparse)(&(g->voltcurmat), c);
-	free(g);
-}
diff --git a/src/graph_genfunc.c b/src/graph_genfunc.c
deleted file mode 100644
index d396206..0000000
--- a/src/graph_genfunc.c
+++ /dev/null
@@ -1,19 +0,0 @@
-
-#include "fracture.h"
-
-double *genfunc_uniform(uint_t num, gsl_rng *r) {
-	double *lattice = (double *)malloc(2 * num * sizeof(double));
-
-	for (uint_t i = 0; i < 2 * num; i++) {
-		lattice[i] = gsl_rng_uniform(r);
-	}
-
-	return lattice;
-}
-
-double *genfunc_hyperuniform(uint_t num, gsl_rng *r) {
-	double *lattice = spheres(num, 0.8, 0.5, 0.9, 100, 100000);
-
-	return lattice;
-}
-
diff --git a/src/spheres_poly/box.cpp b/src/spheres_poly/box.cpp
deleted file mode 100644
index 716090d..0000000
--- a/src/spheres_poly/box.cpp
+++ /dev/null
@@ -1,1157 +0,0 @@
-/* 
-   Updated July 24, 2009 to include hardwall boundary condition option, as 
-   well as polydisperse spheres.  
-
-   Packing of hard spheres via molecular dynamics
-   Developed by Monica Skoge, 2006, Princeton University
-   Contact: Monica Skoge (mskoge.princeton.edu) with questions
-   This code may be used, modified and distributed freely.
-   Please cite:
-   
-   "Packing Hyperspheres in High-Dimensional Euclidean Spaces"
-   	M. Skoge, A. Donev, F. H. Stillinger and S. Torquato, 2006
-	
-   if you use these codes.	
-*/
-
-#include "box.h"
-#include <iostream>
-#include <math.h>
-#include <stdlib.h>
-#include <time.h>
-#include <iomanip>
-
-//==============================================================
-//==============================================================
-//  Class Box: Fills box with hardspheres to given packing fraction
-//  and evolves spheres using molecular dynamics!
-//==============================================================
-//==============================================================
-
-
-//==============================================================
-// Constructor
-//==============================================================
-box::box(int N_i, double r_i, double growthrate_i, double maxpf_i, 
-	 double bidispersityratio_i, double bidispersityfraction_i, 
-	 double massratio_i, int hardwallBC_i):
-  r(r_i),          
-  N(N_i),
-  growthrate(growthrate_i),
-  h(N_i+1),
-  maxpf(maxpf_i),
-  bidispersityratio(bidispersityratio_i),
-  bidispersityfraction(bidispersityfraction_i),
-  massratio(massratio_i),
-  hardwallBC(hardwallBC_i)
-{
-  ngrids = Optimalngrids2(r);
-  cells.set_size(ngrids);
- 
-  s = new sphere[N];
-  binlist = new int[N];
-  x = new vector<DIM>[N];        
-  h.s = s;
-
-  gtime = 0.;
-  rtime = 0.;
-  ncollisions = 0;
-  ntransfers = 0;
-  nchecks = 0;
-  neventstot = 0;
-  ncycles = 0;
-  xmomentum = 0.; 
-  pressure = 0.;
-  collisionrate = 0.;
-
-  cells.set_size(ngrids);
-  cells.initialize(-1);      // initialize cells to -1
-  srandom(::time(0));        // initialize the random number generator
-  for (int i=0; i<N; i++)    // initialize binlist to -1
-    binlist[i] = -1;
-  
-  time(&start);
-}
-
-
-//==============================================================
-// Destructor
-//==============================================================
-box::~box() 
-{
-  delete[] s;
-  delete[] binlist;
-  delete[] x;
-}
-
-
-//==============================================================
-// ReadFile
-//==============================================================
-void box::ReadPositions(const char* filename)
-{  
-  // open file to read in arrays
-  std::ifstream infile(filename);
-  
-  infile.ignore(256, '\n');  // ignore the dim line
-  infile.ignore(256, '\n');  // ignore the #sphere 1 line
-  infile.ignore(256, '\n');  // ignore the #sphere line
-  infile.ignore(256, '\n');  // ignore the diameter line
-  infile.ignore(1000, '\n'); // ignore the 100 010 001 line
-  infile.ignore(256, '\n');  // ignore the T T T line
-
-  for (int i=0; i<N; i++)
-    {
-      infile >> s[i].r;      // read in radius    
-      infile >> s[i].gr;     // read in growth rate
-      infile >> s[i].m;      // read in mass
-      for (int k=0; k<DIM; k++)  
-	infile >> s[i].x[k]; // read in position 
-    }
-  infile.close();
-}
-
-
-//==============================================================
-// Recreates all N spheres at random positions
-//==============================================================
-void box::RecreateSpheres(const char* filename, double temp)
-{
-  ReadPositions(filename);  // reads in positions of spheres
-  VelocityGiver(temp);      // gives spheres initial velocities
-  AssignCells();            // assigns spheres to cells
-  SetInitialEvents();
-}
-
-
-//==============================================================
-// Creates all N spheres at random positions
-//==============================================================
-void box::CreateSpheres(double temp)
-{
-  int Ncurrent = 0;
-  for(int i=0; i<N; i++)
-    {
-      CreateSphere(Ncurrent);
-      Ncurrent++;
-    }
-  if (Ncurrent != N)
-    std::cout << "problem! only made " << Ncurrent << " out of " << N << " desired spheres" << std::endl;
-  
-  VelocityGiver(temp);
-  SetInitialEvents();
-}
-
-   
-//==============================================================
-// Creates a sphere of random radius r at a random unoccupied position 
-//==============================================================
-void box::CreateSphere(int Ncurrent)
-{
-  int keeper;    // boolean variable: 1 means ok, 0 means sphere already there
-  int counter = 0;   // counts how many times sphere already exists
-  vector<DIM> xrand;  // random new position vector
-  double d = 0.;
-  double radius;
-  double growth_rate;
-  double mass;
-  int species;
-  
-  if (Ncurrent < bidispersityfraction*N)
-    {
-      radius = r;
-      growth_rate = growthrate;
-      mass = 1.;
-      species = 1;
-    }
-  else
-    {
-      radius = r*bidispersityratio;
-      growth_rate = growthrate*bidispersityratio;
-      mass = massratio;
-      species = 2;
-    }
-  
-  while (counter<1000)
-    {
-      keeper = 1;
-      
-      for(int k=0; k<DIM; k++) 
-	xrand[k] = ((double)random()/(double)RAND_MAX)*SIZE;
-      
-      for (int i=0; i<Ncurrent; i++)  // check if overlapping other spheres
-	{
-	  d=0.;
-	  if (hardwallBC)
-	    {
-	      for (int k=0; k<DIM; k++) 
-		{     
-		  d += (xrand[k] - s[i].x[k])*(xrand[k] - s[i].x[k]);
-		}
-	    }
-	  else
-	    {
-	      for (int k=0; k<DIM; k++)
-		{
-		  if ((xrand[k] - s[i].x[k])*(xrand[k] - s[i].x[k]) > SIZE*SIZE/4.)
-		    {
-		      if (xrand[k] > SIZE/2.)  // look at right image
-			d += (xrand[k] - (s[i].x[k]+SIZE))*
-			  (xrand[k] - (s[i].x[k]+SIZE));
-		      else                     // look at left image
-			d += (xrand[k] - (s[i].x[k]-SIZE))*
-			  (xrand[k] - (s[i].x[k]-SIZE));
-		    }
-		  else
-		    d += (xrand[k] - s[i].x[k])*(xrand[k] - s[i].x[k]);
-		}
-	    }
-	  if (d <= (radius + s[i].r)*(radius + s[i].r)) // overlapping!
-	    {
-	      keeper = 0;
-	      counter++;
-	      break;
-	    }
-	}
-      
-      if (hardwallBC)
-	{
-	  for (int k=0; k<DIM; k++)    // check if overlapping wall
-	    {     
-	      if ((xrand[k] <= radius) || (SIZE - xrand[k] <= radius)) // touching wall
-		{
-		  keeper = 0;
-		  counter++; 
-		  break;
-		}
-	    }
-	}
-      
-      if (keeper == 1)
-	break;   
-      
-      if (counter >= 1000)
-	{
-	  std::cout << "counter >= 1000" << std::endl;
-	  exit(-1);
-	}
-    }
-
-  // now convert xrand into index vector for cells
-  vector<DIM,int> cell;
-  cell = vector<DIM>::integer(xrand*((double)(ngrids))/SIZE);
-  
-  s[Ncurrent] = sphere(Ncurrent, xrand, cell, gtime, radius, growth_rate, 
-		       mass, species);
-  
-  //first check to see if entry at cell
-  if (cells.get(cell) == -1) //if yes, add Ncurrent to cells gridfield
-    cells.get(cell) = Ncurrent;
-
-  else  // if no, add i to right place in binlist
-    {  
-      int iterater = cells.get(cell); // now iterate through to end and add Ncurrent
-      int pointer = iterater;
-      while (iterater != -1)
-	{
-	  pointer = iterater;
-	  iterater = binlist[iterater];
-	}
-      binlist[pointer] = Ncurrent;
-    }
-
-}
-
-
-//==============================================================
-// Assign cells to spheres read in from existing configuration
-//==============================================================
-void box::AssignCells()
-{
-  for (int i=0; i<N; i++)
-    {
-      // now convert x into index vector for cells
-      vector<DIM,int> cell;
-      cell = vector<DIM>::integer(s[i].x*((double)(ngrids))/SIZE);
-      s[i].cell = cell;
-      
-      //first check to see if entry at cell
-      if (cells.get(cell) == -1) //if yes, add Ncurrent to cells gridfield
-	cells.get(cell) = i;
-      
-      else  // if no, add i to right place in binlist
-	{  
-	  int iterater = cells.get(cell); // now iterate through to end and add Ncurrent
-	  int pointer = iterater;
-	  while (iterater != -1)
-	    {
-	      pointer = iterater;
-	      iterater = binlist[iterater];
-	    }
-	  binlist[pointer] = i;
-	}
-    }
-}
-
-	
-//==============================================================
-// Velocity Giver, assigns initial velocities from Max/Boltz dist.
-//==============================================================
-void box::VelocityGiver(double T)
-{
-  for (int i=0; i<N; i++)
-    {
-      for (int k=0; k<DIM; k++)
-	{
-	  if (T==0.)
-	    s[i].v[k] = 0.;
-	  else
-	    s[i].v[k] = Velocity(T);
-	}
-    }
-}
-
-
-//==============================================================
-// Velocity, gives a single velocity from Max/Boltz dist.
-//==============================================================
-double box::Velocity(double T)
-{
-  double rand;                       // random number between -0.5 and 0.5
-  double sigmasquared = T;    // Assumes M = mass of sphere = 1
-  double sigma = sqrt(sigmasquared); // variance of Gaussian
-  double stepsize = 1000.;           // stepsize for discretization of integral
-  double vel = 0.0;                  // velocity
-  double dv=sigma/stepsize;
-  double p=0.0;
-  
-  rand = (double)random() / (double)RAND_MAX - 0.5;
-  if(rand < 0) 
-    {
-      rand = -rand;
-      dv = -dv;
-    }
-  
-  while(fabs(p) < rand) // integrate until the integral equals rand
-    {
-      p += dv * 0.39894228 * exp(-vel*vel/(2.*sigmasquared))/sigma;
-      vel += dv;
-    }
-  return vel;
-}
-
-
-//==============================================================
-// Finds next events for all spheres..do this once at beginning
-//==============================================================
-void box::SetInitialEvents()
-{
-  for (int i=0; i<N; i++)  // set all events to checks
-    {
-      event e(gtime, i, INF); 
-      s[i].nextevent = e;
-      h.insert(i);
-    }
-}
-
-
-//==============================================================
-// Finds next event for sphere i 
-//==============================================================
-event box::FindNextEvent(int i)
-{
-  double outgrowtime;
-  outgrowtime = (.5/ngrids - (s[i].r+s[i].gr*gtime))/s[i].gr + gtime;
-
-  event t = FindNextTransfer(i);
-  event c = FindNextCollision(i);
-
-  if ((outgrowtime < c.time)&&(outgrowtime < t.time)&&(ngrids>1))
-    {
-      event o = event(outgrowtime,i,INF-1);
-      return o;
-    }
-
-  if ((c.time < t.time)&&(c.j == INF)) // next event is check at DBL infinity
-    return c;
-  else if (c.time < t.time) // next event is collision!
-    {
-      CollisionChecker(c); 
-      return c; 
-    }
-  else // next event is transfer!
-    return t;  
-} 
-
-
-//==============================================================
-// Checks events of predicted collision partner to keep collisions
-// symmetric
-//==============================================================
-void box::CollisionChecker(event c)
-{
-  int i = c.i;
-  int j = c.j;
-  event cj(c.time,j,i,c.v*(-1));
-
-  // j should have NO event before collision with i!
-  if (!(c.time  < s[j].nextevent.time))
-    std::cout << i << " " <<  j << " error collchecker, s[j].nextevent.time= " << s[j].nextevent.time << " " << s[j].nextevent.j << ", c.time= " << c.time << std::endl;
-  
-  int k = s[j].nextevent.j; 
-  if ((k < N) && (k!=i)) // j's next event was collision so give k a check
-    s[k].nextevent.j = INF;
-  
-  // give collision cj to j
-  s[j].nextevent = cj;
-  h.upheap(h.index[j]);
-}
-
-
-//==============================================================
-// Find next transfer for sphere i 
-//==============================================================
-event box::FindNextTransfer(int i)
-{
-  double ttime = dblINF;  
-  int wallindex = INF;   // -(k+1) left wall, (k+1) right wall
-
-  vector<DIM> xi = s[i].x + s[i].v*(gtime - s[i].lutime);
-  vector<DIM> vi = s[i].v;
-
-  for (int k=0; k<DIM; k++)
-    {
-      double newtime;
-      if (vi[k]==0.) 
-	newtime= dblINF;
-      else if (vi[k]>0)  // will hit right wall, need to check if last wall
-	{
-	  if ((hardwallBC)&&(s[i].cell[k] == ngrids - 1))
-	    newtime = ((double)(s[i].cell[k]+1)*SIZE/((double)(ngrids))
-		       - (xi[k]+s[i].r+s[i].gr*gtime))/(vi[k]+s[i].gr);
-	  else
-	    newtime = ((double)(s[i].cell[k]+1)*SIZE/((double)(ngrids))
-		       - xi[k])/(vi[k]);
-	  
-	  if (newtime<ttime)
-	    {
-	      wallindex = k+1;
-	      ttime = newtime;
-	    }
-	}
-      else if (vi[k]<0)  // will hit left wall
-	{
-	  if ((hardwallBC)&&(s[i].cell[k] == 0))
-	    newtime = ((double)(s[i].cell[k])*SIZE/((double)(ngrids)) 
-		       - (xi[k]-(s[i].r+s[i].gr*gtime)))/(vi[k]-s[i].gr);
-	  else
-	    newtime = ((double)(s[i].cell[k])*SIZE/((double)(ngrids)) 
-		       - xi[k])/(vi[k]);
-	  
-	  if (newtime<ttime)
-	    {
-	      wallindex = -(k+1);
-	      ttime = newtime;
-	    }
-	}
-    }
-  
-
-  if (ttime < 0)
-    ttime = 0;
-  // make the event and return it
-  event e = event(ttime+gtime,i,wallindex+DIM+N+1);
-  return e;
-}
-
-
-//==============================================================
-// Check all nearest neighbor cells for collision partners
-//==============================================================
-void box::ForAllNeighbors(int i, vector<DIM,int> vl, vector<DIM,int> vr,
-			  neighbor& operation)
-{
-  vector<DIM,int> cell = s[i].cell;
-
-  // now iterate through nearest neighbors
-  vector<DIM, int> offset;          // nonnegative neighbor offset
-  vector<DIM, int> pboffset;        // nearest image offset
-
-   vector<DIM,int> grid;
-
-   int ii ;
-
-   grid=vl;
-   while(1)
-   {
-     //if (vr[0] > 1)
-     //std::cout << grid << "..." << cell+grid << "\n";
-     for(int k=0; k<DIM; k++)
-     {
-        offset[k]=grid[k]+ngrids;  // do this so no negatives 	
-        if (cell[k]+grid[k]<0) //out of bounds to left
-          pboffset[k] = -1;
-	else if (cell[k]+grid[k]>=ngrids) // out of bounds to right
-	  pboffset[k] = 1;
-        else
-          pboffset[k] = 0;
-     }     
-     int j = cells.get((cell+offset)%ngrids);
-     while(j!=-1)
-       {
-	 operation.Operation(j,pboffset);
-	 j = binlist[j];
-       }
-
-     // A. Donev:     
-     // This code makes this loop dimension-independent
-     // It is basically a flattened-out loop nest of depth DIM
-     for(ii=0;ii<DIM;ii++)
-     {
-       grid[ii] += 1;
-       if(grid[ii]<=vr[ii]) break;
-       grid[ii]=vl[ii];
-     }
-     if(ii>=DIM) break;
-   }  
-}
-
-
-//==============================================================
-// PredictCollision
-//==============================================================
-void box::PredictCollision(int i, int j, vector<DIM, int> pboffset, 
-			     double& ctime, int& cpartner, 
-			     vector<DIM, int>& cpartnerpboffset)
-{
-  double ctimej;
-  
-  if (i!=j)
-    {	 
-      ctimej = CalculateCollision(i,j,pboffset.Double())+gtime;
-      
-      if (ctimej < gtime)
-	std::cout << "error in find collision ctimej < 0" << std::endl;
-      
-      if ((ctimej < ctime)&&(ctimej < s[j].nextevent.time))
-	{
-	  ctime = ctimej;
-	  cpartner = j;
-	  cpartnerpboffset = pboffset;
-	}	
-    }
-}
-
-
-//==============================================================
-// Find next collision
-//==============================================================
-event box::FindNextCollision(int i)
-{
-  collision cc(i, this);
-  
-  vector<DIM, int> vl, vr;
-
-  for (int k=0; k<DIM; k++)  // check all nearest neighbors
-    {
-      vl[k] = -1;
-      vr[k] = 1;
-    }
-  
-  ForAllNeighbors(i,vl,vr,cc);
-
-  event e;
-  if (cc.cpartner == i)  // found no collisions in neighboring cells
-    {
-      if (cc.ctime != dblINF)
-	std::cout << "ctime != dblINF" << std::endl;
-      e = event(dblINF,i,INF);  // give check at double INF
-    }
-  else
-    e = event(cc.ctime,i,cc.cpartner,cc.cpartnerpboffset);
-
-  return e;
-}
-
-
-//==============================================================
-// Calculates collision time between i and image of j using quadratic formula
-//==============================================================
-double box::CalculateCollision(int i, int j, vector<DIM> pboffset)
-{
-  if ((hardwallBC)&&(pboffset.norm_squared() > 1E-12))
-    {
-      return dblINF;
-    }
-  else
-    {      
-      // calculate updated position and velocity of i and j
-      vector<DIM> xi = s[i].x + s[i].v*(gtime - s[i].lutime);
-      vector<DIM> vi = s[i].v;
-      vector<DIM> xj = s[j].x + pboffset*SIZE + s[j].v*(gtime - s[j].lutime);
-      vector<DIM> vj = s[j].v;
-      
-      double r_now_i = s[i].r + gtime*s[i].gr;
-      double r_now_j = s[j].r + gtime*s[j].gr;
-      
-      double A,B,C;
-      A = vector<DIM>::norm_squared(vi - vj) - (s[i].gr+s[j].gr)*(s[i].gr+s[j].gr);
-      B = vector<DIM>::dot(xi - xj, vi - vj) - (r_now_i+r_now_j)*(s[i].gr+s[j].gr);
-      C = vector<DIM>::norm_squared(xi - xj) - (r_now_i+r_now_j)*(r_now_i+r_now_j);
-
-      if (C < -1E-12*(r_now_i+r_now_j))
-	{
-	  std::cout << "error, " << i << " and " << j << 
-	    " are overlapping at time "<< gtime << std::cout;
-	  std::cout << "A, B, C = "  << A << " " << " " << B << 
-	    " " << " " << C <<  std::endl;
-	  if (CheckSphereDiameters()>0)
-	    std::cout << "a sphere has grown greater than unit cell" << 
-	      std::endl;
-	  else
-	    std::cout << "unknown error" << std::cout;
-	  exit(-1);
-	}
-      
-      return QuadraticFormula(A, B, C);
-    }  
-}
-
-
-//==============================================================
-// Quadratic Formula ax^2 + bx + c = 0
-//==============================================================
- double box::QuadraticFormula(double a, double b, double c)
-{
-  double x = dblINF;
-  double xpos;
-  double xneg;
-  double det = b*b - a*c;
-
-  if (c <= 0.)
-    {
-      if(b < 0.) // spheres already overlapping and approaching
-	{
-	  //std::cout << "spheres overlapping and approaching" << std::endl;
-	  //std::cout << "# events= " << neventstot << std::endl;
-	  x = 0.;	
-	}
-    }
-  else if (det > -10.*DBL_EPSILON)
-    {
-      if (det < 0.)  // determinant can be very small for double roots
-	det = 0.;    
-      if (b < 0.)
-	x = c/(-b + sqrt(det));
-      else if ((a < 0.)&&(b > 0.))
-	x = -(b + sqrt(det))/a;
-      else
-	x = dblINF;
-    }
-  return x;
-}
-
-
-//==============================================================
-// Returns first event
-//==============================================================
-void box::ProcessEvent()
-{  
-  neventstot++;
-  // Extract first event from heap
-  int i = h.extractmax();   
-  event e = s[i].nextevent; // current event
-  event f;                  // replacement event
-
-  if ((e.j>=0)&&(e.j<N))  // collision!
-    {
-      ncollisions++;
-      //std::cout << "collision between " << e.i << " and " << e.j << " at time " << e.time << std::endl;
-      Collision(e);
-      f = FindNextEvent(i);
-      s[i].nextevent = f;
-      h.downheap(1);
-      if (f.time < e.time)
-	{
-	  std::cout << "error, replacing event with < time" << std::endl;
-	  exit(-1);
-	}
-      
-      // make sure collision was symmetric and give j a check
-      if ((s[e.j].nextevent.j != i)||(s[e.j].nextevent.time != gtime))
-	{
-	  std::cout << "error collisions not symmetric" << std::endl;
-	  std::cout << "collision between " << e.i << " and " << e.j << " at time " << e.time << std::endl;
-	  std::cout << "but " << e.j << " thinks it has " << s[e.j].nextevent.j<< " "  << s[e.j].nextevent.time << std::endl;
-	  exit(-1);
-	}
-      else  // give j a check
-	s[e.j].nextevent.j = INF;
-    }
-  else if (e.j==INF)      // check!  
-    {
-      nchecks++;
-      //std::cout << "check for " << e.i << " at time " << e.time << std::endl;
-      f = FindNextEvent(i);
-      s[i].nextevent = f;
-      h.downheap(1);
-    }
-  else if (e.j==INF-1)      // sphere outgrowing unit cell, decrease ngrids!
-    {
-      gtime = e.time;
-      Synchronize(false);
-      ngrids = ngrids - 1;
-//      std::cout << "need to reduce ngrids to " << ngrids << std::endl;   
-      ChangeNgrids(ngrids);
-      h.downheap(1);
-    }
-  else                    // transfer!
-    {
-      ntransfers++;
-      //std::cout << "transfer for " << e.i << " at time " << e.time << std::endl;
-      Transfer(e);
-      f = FindNextEvent(i);
-      s[i].nextevent = f;
-      h.downheap(1);
-      //r = FindNextEvent(i, e.j-N-DIM-1);
-      //if (f.time <= e.time)
-      if (f.time < e.time)
-	{
-	  std::cout << "error after transfer, replacing new event with < time" << " " << std::endl;
-	  std::cout << std::setprecision(16) << "e.time= " << e.time << ", f.time= " << f.time << ", f.i= " << f.i << ", f.j= " << f.j << "e.i= " << e.i << ", e.j= " << e.j << std::endl;
-	  std::cout << std::setprecision(16) << "difference= " << e.time - f.time << std::endl;
-	  exit(-1);
-	}
-    }
-}
-
-
-//==============================================================
-// Processes a collision
-//=============================================================
-void box::Collision(event e)
-{
-  double ctime = e.time;
-  int i = e.i;
-  int j = e.j;
-  vector<DIM,int> v = e.v;  // virtual image
-  gtime = ctime;
-
-  // Update positions and cells of i and j to ctime
-  s[i].x += s[i].v*(gtime-s[i].lutime);
-  s[j].x += s[j].v*(gtime-s[j].lutime);
-
-  // Check to see if a diameter apart
-  double r_sum = s[i].r + s[j].r + (s[i].gr+s[j].gr)*gtime;
-  double distance = vector<DIM>::norm_squared(s[i].x - s[j].x- v.Double()*SIZE) - r_sum*r_sum;
-  if (distance*distance > 10.*DBL_EPSILON)
-    std::cout << "overlap " << distance << std::endl;
-
-  s[i].lutime = gtime;
-  s[j].lutime = gtime;
-  
-  vector<DIM,double> vipar;          // parallel comp. vi
-  vector<DIM,double> vjpar;          // parallel comp. vj
-  vector<DIM,double> viperp;         // perpendicular comp. vi
-  vector<DIM,double> vjperp;         // perpendicular comp. vj
-
-  // make unit vector out of displacement vector
-  vector<DIM,double> dhat;
-  dhat = s[i].x - s[j].x - v.Double()*SIZE;  // using image of j!!
-  double dhatmagnitude = sqrt(dhat.norm_squared());
-  dhat /= dhatmagnitude;
-
-  vipar = dhat*vector<DIM>::dot(s[i].v, dhat);
-  vjpar = dhat*vector<DIM>::dot(s[j].v, dhat);
-  viperp = s[i].v - vipar;
-  vjperp = s[j].v - vjpar;
-
-  s[i].v = vjpar + dhat*(s[i].gr+s[j].gr)*2 + viperp;
-  s[j].v = vipar - dhat*(s[i].gr+s[j].gr)*2 + vjperp;
-
-  // momentum exchange
-  double xvelocity;   // exchanged velocity
-  xvelocity = vector<DIM>::dot(s[i].v - s[j].v, dhat) - (s[i].gr+s[j].gr);
-  xmomentum += xvelocity*dhatmagnitude*s[i].m*s[j].m*2/(s[i].m+s[j].m);
-}
-
-
-//==============================================================
-// Transfer, takes care of boundary events too
-//=============================================================
-void box::Transfer(event e)
-{
-  gtime = e.time;
-  int i = e.i;
-  int j = e.j;
-  int k=0;           // dimension perpendicular to wall it crosses
- 
-  // update position and lutime (velocity doesn't change)
-  s[i].x += s[i].v*(gtime-s[i].lutime);
-  s[i].lutime = gtime;
-
-  vector<DIM,int> celli;  // new cell for i
-  celli = s[i].cell;  // this is not redundant
-  
-  // update cell
-  if (j>N+DIM+1)  // right wall
-    {
-      k = j-N-DIM-2;
-      celli[k] = s[i].cell[k] + 1;
-
-      if (hardwallBC)
-	{
-	  // if in right-most cell, reflect back
-	  if (s[i].cell[k] == ngrids - 1)
-	    s[i].v[k] = -s[i].v[k] - 4.*s[i].gr;
-	  else
-	    {
-	      if (ngrids>1)
-		UpdateCell(i, celli); 
-	    }
-	}
-      else
-	{
-	  // if in right-most cell, translate x and cell
-	  if (s[i].cell[k] == ngrids - 1)
-	    {
-	      s[i].x[k] -= SIZE;
-	      celli[k] -= ngrids;
-	    }
-	  if (ngrids>1)
-	    UpdateCell(i, celli); 
-	}
-    }
-  else if (j<N+DIM+1)  // left wall
-    {
-      k = -j+N+DIM;
-      celli[k] = s[i].cell[k] - 1;
-
-      if (hardwallBC)
-	{
-	  // if in left-most cell, reflect back
-	  if (s[i].cell[k] == 0)
-	    s[i].v[k] = -s[i].v[k] + 4.*s[i].gr;
-	  else
-	    {
-	      if (ngrids>1)
-		UpdateCell(i, celli); 
-	    }
-	}
-      else
-	{
-	  // if in left-most cell, translate x and cell
-	  if (s[i].cell[k] == 0)
-	    {
-	      s[i].x[k] += SIZE;
-	      celli[k] += ngrids;
-	    }
-	  if (ngrids>1)
-	    UpdateCell(i, celli); 
-	}
-    }
-  else
-    std::cout << "error in Transfer" << std::endl;    
-  
-}
-
-
-//==============================================================
-// Updates cell of a sphere to time
-//=============================================================
-void box::UpdateCell(int i, vector<DIM,int>& celli)
-{
-  if (celli == s[i].cell)
-    std::cout << "error in update cell..shouldn't be the same" << std::endl;
-  
-  // delete i from cell array at cell
-
-  if (cells.get(s[i].cell) == i) 
-    {
-      if (binlist[i] == -1)
-	cells.get(s[i].cell) = -1;
-      else
-	{
-	  cells.get(s[i].cell) = binlist[i];
-	  binlist[i] = -1;
-	}
-    }
-
-  else if (cells.get(s[i].cell) == -1)
-    {
-      std::cout << "error " << i << " not in claimed cell UpdateCell" << std::endl;
-      OutputCells();
-    }
-
-  else  // if no, find i in binlist
-    {  
-      int iterater = cells.get(s[i].cell);
-      int pointer = iterater;
-      while ((iterater != i)&&(iterater != -1))
-	{
-	  pointer = iterater;
-	  iterater = binlist[iterater];
-	}
-      if (iterater == -1)  // got to end of list without finding i
-	{
-	  std::cout << "problem " << i << " wasn't in claimed, cell iterater = -1" << std::endl;
-	  OutputCells();
-	}
-      else  // we found i!
-	{
-	  binlist[pointer] = binlist[i]; 
-	  binlist[i] = -1;
-	}	  
-    } 
-
-  // now add i to cell array at celli
-  s[i].cell = celli;
-  
-  //first check to see if entry at celli
-  if (cells.get(celli) == -1) //if yes, add i to cells gridfield
-    cells.get(celli) = i;
-  else  // if no, add i to right place in binlist
-    {
-      int iterater = cells.get(celli);  // now iterate through to end and add i
-      int pointer = iterater;
-      while (iterater != -1)  // find the end of the list
-	{
-	  pointer = iterater;
-	  iterater = binlist[iterater];
-	}
-      binlist[pointer] = i;
-      binlist[i] = -1; // redundant
-    }
-}
-
-
-//==============================================================
-// Output event heap...purely used for debugging
-//==============================================================
-void box::OutputEvents()
-{
-  h.print();
-}
-
-
-//==============================================================
-// Output positions of spheres and their cells...purely used for debugging
-//==============================================================
-void box::OutputCells()
-{
-  for (int i=0; i<N; i++)
-    std::cout << i << " " << s[i].x << " " << s[i].v << " " << s[i].cell << std::endl;
-}
-
-
-//==============================================================
-// Update positions...purely for graphical display
-//==============================================================
-void box::TrackPositions()
-{
-  for (int i=0; i<N; i++)
-    x[i] = s[i].x + s[i].v*(gtime-s[i].lutime);
-}
-
-
-//==============================================================
-// Computes the total energy
-//==============================================================
-double box::Energy()
-{
-  double E=0;
-  for (int i=0; i<N; i++)
-    E += 0.5*s[i].m*s[i].v.norm_squared();
-
-  return E/N;
-}
-
-
-//==============================================================
-// Calculates the packing fraction
-//==============================================================
-double box::PackingFraction()
-{
-  double rfactor = 0.;
-  for (int i=0; i<N; i++)
-    {
-      rfactor += pow(s[i].r + gtime*s[i].gr, DIM);
-    }
-  double v = (rfactor*pow(sqrt(PI), DIM))/(exp(lgamma(1.+((double)(DIM))/2.)));
-  return v/(pow(SIZE, DIM));
-}
-
-
-//==============================================================
-// Checks to make sure all sphere diameters are less than dimension
-// of unit cell
-//==============================================================
-int box::CheckSphereDiameters()
-{
-  int offender = 0;
-  for (int i=0; i<N; i++)
-    {
-      if (s[i].r*2 > 1./ngrids){
-	offender = i;
-	break;
-      }
-    }
-  return offender;
-}
-
-
-//==============================================================
-// Change ngrids
-//==============================================================
-void box::ChangeNgrids(int newngrids)
-{
-  cells.set_size(newngrids);
-  cells.initialize(-1);      // initialize cells to -1
-  for (int i=0; i<N; i++)    // initialize binlist to -1
-    binlist[i] = -1;
-  AssignCells();
-  for (int i=0; i<N; i++)
-    s[i].nextevent = event(0., i, INF); 
-  Process(N); 
-}	 
-
-
-//==============================================================
-// Calculates the optimal ngrids for the initial configuration
-// and assumes that ngrids gets updated (reduced) as the packing
-// proceeds
-//==============================================================
-int box::Optimalngrids2(double currentradius)
-{
-  return (int)(1./(2.*currentradius));
-}
-
-
-//==============================================================
-// Calculates the optimal ngrids, assuming ngrids is not updated
-// automatically and is very conservative
-//==============================================================
-int box::Optimalngrids()
-{
-  double maxr;
-
-  maxr = pow(exp(lgamma(1.+((double)(DIM))/2.))*maxpf/
-	     (N*(bidispersityfraction + (1.-bidispersityfraction)*
-		 pow(bidispersityratio, DIM))), 
-	     1./DIM)/sqrt(PI);
-
-  return (int)(1./(2.*maxr));
-}
-
-
-//==============================================================
-// Processes n events
-//==============================================================
-void box::Process(int n)
-{
-  double deltat = gtime;
-  for (int i=0; i<n; i++)
-    {
-      ProcessEvent();
-    }
-  pf = PackingFraction();   // packing fraction
-  deltat = gtime - deltat;
-  double oldenergy = energy;
-  energy = Energy();        // kinetic energy
-
-  energychange = ((oldenergy - energy)/oldenergy)*100; // percent change in energy
-
-  if (deltat != 0.)
-    {
-      pressure = 1+xmomentum/(2.*energy*N*deltat);
-      collisionrate = ((double)(ncollisions))/deltat;
-    }  
-
-  // reset to 0
-  ncollisions = 0;
-  ntransfers = 0;
-  nchecks = 0;
-  xmomentum = 0.;
-  ncycles++;
-}
-
-
-//==============================================================
-// Prints statistics for n events
-//==============================================================
-void box::PrintStatistics()
-{
-  std::cout << "packing fraction = " << pf << std::endl;
-  std::cout << "gtime = " << gtime << std::endl; 
-  std::cout << "total time = " << rtime+gtime << std::endl;
-  std::cout << "kinetic energy = " << energy << std::endl;
-  std::cout << "total # events = " << neventstot << std::endl;
-  std::cout << "# events = " << ncollisions+ntransfers+nchecks << ", # collisions = " << ncollisions << ", # transfers = " << ntransfers << ", # checks =" << nchecks << std::endl;
-  std::cout << "growthrate = " << growthrate << std::endl;
-  std::cout << "collisionrate = " << collisionrate << std::endl;
-  std::cout << "reduced pressure = " << pressure << std::endl;
-  std::cout << "-----------------" << std::endl;
-}
-
-
-//==============================================================
-// Updates spheres to gtime, synchronizes, and can change growth rate
-//==============================================================
-void box::Synchronize(bool rescale)
-{
-  double vavg = sqrt(2.*M*energy);
-
-  for (int i=0; i<N; i++)
-    {
-      s[i].x = s[i].x + s[i].v*(gtime-s[i].lutime);
-      s[i].nextevent.time -= gtime;
-
-      if (s[i].nextevent.time < 0.)
-	std::cout << "error, event times negative after synchronization" << std::endl;
-      if (rescale == true)   // give everyone checks
-	{
-	  s[i].nextevent = event(0., i, INF); 
-	  s[i].v /= vavg;
-	}
-	  
-      s[i].lutime = 0.;
-      s[i].r += gtime*s[i].gr;   
-    }
-
-  //r += gtime*growthrate;       // r defined at gtime = 0
-  rtime += gtime;
-  gtime = 0.;
-  
-  if (rescale == true)
-    Process(N);
-}
-
-
-//==============================================================
-// Run time
-//==============================================================
-void box::RunTime()
-{
-  time(&end);
-  std::cout << "run time = " << difftime(end, start) << std::endl;
-}
-
-
-//==============================================================
-// Write configuration
-//==============================================================
-void box::WriteConfiguration(double *data)
-{
-  int count1;
-
-  if (gtime != 0.)   // synchronize spheres if not currently synchronized
-    Synchronize(false);
-      
-  
- for (int i=0; i<N; i++)  // output radius and positions
-   {
-     for (int k=0; k<DIM; k++)
-			 data[DIM * i + k] = s[i].x[k];
-   }
- 
-}
diff --git a/src/spheres_poly/box.h b/src/spheres_poly/box.h
deleted file mode 100644
index 69418f4..0000000
--- a/src/spheres_poly/box.h
+++ /dev/null
@@ -1,169 +0,0 @@
-/* 
-   Packing of hard spheres via molecular dynamics
-   Developed by Monica Skoge, 2006, Princeton University
-   Contact: Aleksandar Donev (adonev@math.princeton.edu) with questions
-   This code may be used, modified and distributed freely.
-   Please cite:
-   
-   "Packing Hyperspheres in High-Dimensional Euclidean Spaces"
-   	M. Skoge, A. Donev, F. H. Stillinger and S. Torquato, 2006
-	
-   if you use these codes.	
-*/
-
-//-----------------------------------------------------------------------------
-// Box maker
-//---------------------------------------------------------------------------
-
-#ifndef  BOX_H
-#define  BOX_H
-
-
-#include <vector>
-#include <math.h>
-
-#include "vector.h"
-#include "grid_field.h"
-#include "event.h"
-#include "sphere.h"
-#include "heap.h"
-
-
-#define PI     3.141592653589793238462643
-#define SIZE   1.0            // size of box
-#define VOLUMESPHERE pow(PI,((double)(DIM))/2.)/exp(lgamma(1+((double)(DIM))/2.)) // volume prefactor for sphere
-#define DBL_EPSILON  2.2204460492503131e-016 // smallest # such that 1.0+DBL_EPSILON!=1.0
-#define M 1.0
-
-//---------------------------------------------------------------------------
-// Class neighbor
-//---------------------------------------------------------------------------
-class neighbor
-{
- public:
-  int i;
-  
-  neighbor(int i_i);
-
- public:
-  virtual void Operation(int j, vector<DIM, int>& pboffset) = 0;
-};
-
-
-class box {
-  
- public:
-  
-  // constructor and destructor
-  box(int N_i, double r_i, double growthrate_i, double maxpf_i, 
-      double bidispersityratio, double bidispersityfraction, 
-      double massratio, int hardwallBC);
-  ~box();
-
-  // Creating configurations
-  int Optimalngrids();
-  int Optimalngrids2(double maxr);
-  void CreateSpheres(double temp);
-  void CreateSphere(int Ncurrent);   
-  double Velocity(double temp);
-  void VelocityGiver(double temp);  
-  void SetInitialEvents();
-  void RecreateSpheres(const char* filename, double temp);
-  void ReadPositions(const char* filename);
-  void AssignCells();
- 
-  // Predicting next event
-  event FindNextEvent(int i);
-  void CollisionChecker(event c);
-  event FindNextTransfer(int i);
-  event FindNextCollision(int i);
-  void ForAllNeighbors(int, vector<DIM, int>, vector<DIM,int>, neighbor&);
-  void PredictCollision(int i, int j, vector<DIM, int> pboffset, 
-			double& ctime, int& cpartner, 
-			vector<DIM, int>& cpartnerpboffset);
-  double CalculateCollision(int i, int j, vector<DIM>  pboffset);
-  double QuadraticFormula(double a, double b, double c);
-  
-  // Processing an event
-  void Process(int n);
-  void ProcessEvent();
-  void Collision(event e);
-  void Transfer(event e);
-  void UpdateCell(int i, vector<DIM,int>& celli);
-  void Synchronize(bool rescale);
-  void ChangeNgrids(int newngrids);
-
-  // Debugging
-  void TrackPositions();
-  void OutputEvents();
-  void OutputCells();
-  void GetInfo();  
-  int CheckSphereDiameters();
-
-  // Statistics
-  double Energy();
-  double PackingFraction();  
-  void PrintStatistics();
-  void RunTime();
-  void WriteConfiguration(double* data);
-  
-  
-  //variables
-
-  const int N;                   // number of spheres
-  
-  int ngrids;                    // number of cells in one direction
-  double maxpf;
-  double growthrate;             // growth rate of the spheres
-  double r;                      // radius, defined at gtime = 0
-  double gtime;                  // this is global clock
-  double rtime;                  // reset time, total time = rtime + gtime
-  double collisionrate;          // average rate of collision between spheres
-  double bidispersityratio;      // ratio of sphere radii
-  double bidispersityfraction;   // fraction of smaller spheres
-  double massratio;              // ratio of sphere masses
-  int hardwallBC;                // =0 for periodic BC, =1 for hard wall
-  
-
-  // statistics
-  double pressure;               // pressure
-  double xmomentum;              // exchanged momentum
-  double pf;                     // packing fraction
-  double energy;                 // kinetic energy
-  double energychange;
-  int ncollisions;               // number of collisions
-  int ntransfers;                // number of transfers
-  int nchecks;                   // number of checks
-  int neventstot;                // total number of events 
-  int ncycles;                   // counts # cycles for output
-
-  time_t start, error, end;      // run time of program
-
-  // arrays
-  sphere *s;                      // array of spheres
-  grid_field<DIM, int> cells; // array that keeps track of spheres in each cell
-  int *binlist;                   // linked-list for cells array
-  heap h;                         // event heap
-  vector<DIM> *x;                 // positions of spheres.used for graphics
-};
-
-
-//---------------------------------------------------------------------------
-// Predicts collisions, inherits neighbor operation
-//---------------------------------------------------------------------------
-class collision : public neighbor 
-{
- public:
-  
-  box *b; 
-  double ctime;
-  int cpartner;
-  vector<DIM,int> cpartnerpboffset;
-
- public:
-  collision(int i_i, box *b);
-
-  virtual void Operation(int j, vector<DIM, int>& pboffset);
-};
-
-#endif 
diff --git a/src/spheres_poly/event.cpp b/src/spheres_poly/event.cpp
deleted file mode 100644
index c8c104d..0000000
--- a/src/spheres_poly/event.cpp
+++ /dev/null
@@ -1,65 +0,0 @@
-#include "event.h" 
-
-//==============================================================
-//==============================================================
-//  Class Event 
-//==============================================================
-//==============================================================
-
-
-//==============================================================
-// Constructor
-//==============================================================
-event::event(double time_i, int i_i, int j_i, vector<DIM,int> v_i):
-  time(time_i),
-  i(i_i),
-  j(j_i),
-  v(v_i)
-{
-}
-
-event::event(double time_i, int i_i, int j_i):
-  time(time_i),
-  i(i_i),
-  j(j_i)
-{
-}
-
-event::event(const event& e)
-{
-  time = e.time;
-  i = e.i;
-  j = e.j;
-  v = e.v;
-}
-
-event::event()
-{
-}
-
-  
-//==============================================================
-// Destructor
-//==============================================================
-event::~event() 
-{
-}
-
-void event::erase()
-{
-  time = dblINF;
-  i = 0;
-  j = 0;
-}
-
-bool event::operator<(const event& e) const
-{
-  return e.time < time;
-}
-
-bool event::operator>(const event& e) const
-{
-  return e.time > time;
-}
-
- 
diff --git a/src/spheres_poly/event.h b/src/spheres_poly/event.h
deleted file mode 100644
index 55dd1fc..0000000
--- a/src/spheres_poly/event.h
+++ /dev/null
@@ -1,58 +0,0 @@
-#ifndef  EVENT_H
-#define  EVENT_H
-
-#include "vector.h"
-#define INF    100000000
-#define dblINF 100000000.
-
-class event {
-
- public:
-
-  // constructor and destructor
-  event(double time_i, int i_i, int j_i, vector<DIM,int> v_i);
-  event(double time_i, int i_i, int j_i);
-  event(const event& e);
-  event();
-  
-  ~event();
-
-  bool operator<(const event&) const;
-  bool operator>(const event&) const;
-  void erase();
-
- //variables
-
-
-  double time;             // time of next collision
-  int i;        // collision partner with lower number
-  int j;        // collision partner with higher number
-  vector<DIM,int> v;        // virtual image
-
-  /* 0<=j<=N                binary collision between i and j
-     j=N+DIM+1+x            transfer where x=-(k+1) for left wall
-                            and x=k+1 for right wall
-     j=INF                 both check after event that did not altered motion of                           i and check after event that altered motion of i, i.e                           rescaling of velocities. I currently don't see need t                           o separate the two
-
-     j=-1                  check after collision
-
-     Virtual identifiers as scalars...I think bad idea, but here's my work
-     there will be easily fixed problems if DIM>=10
-     -x<=v<=x               x=k+1, image in k direction
-     v=xy                   x,y
-      =-xy                  -x,y
-      =-yx                  x,-y
-      =yx                   -x,-y
-     v=xyz                  x,y,z
-      =-xyz                 -x,y,z
-      =-yxz                 x,-y,z
-      =-zxy                 x,y,-z
-      =zyx                  -x,-y,z
-      =xzy                  x,-y,-z
-      =yzx                  -x,y,-z
-      =-zyx                 -x,-y,-z
-  */      
-
-};
-
-#endif 
diff --git a/src/spheres_poly/grid_field.h b/src/spheres_poly/grid_field.h
deleted file mode 100644
index 10430ed..0000000
--- a/src/spheres_poly/grid_field.h
+++ /dev/null
@@ -1,148 +0,0 @@
-/* 
-   Packing of hard spheres via molecular dynamics
-   Developed by Monica Skoge, 2006, Princeton University
-   Contact: Aleksandar Donev (adonev@math.princeton.edu) with questions
-   This code may be used, modified and distributed freely.
-   Please cite:
-   
-   "Packing Hyperspheres in High-Dimensional Euclidean Spaces"
-   	M. Skoge, A. Donev, F. H. Stillinger and S. Torquato, 2006
-	
-   if you use these codes.	
-*/
-
-
-#ifndef GRID_FIELD_H
-#define GRID_FIELD_H
-
-#include "vector.h"
-
-// ======================================================================
-// grid_field 
-// ======================================================================
-
-// A field of V-vectors on a D dimensional manifold
-
-template<int D, class T>
-class grid_field {
-  
- public:
-  int elements;
-
- private:
-  T* f;
-  vector<D, int> size;           // number of grid points for each dimension
-  vector<D, int> offset;
- 
- public:
-
-  grid_field();
-  grid_field(const vector<D, int>&);
-  ~grid_field();
-
-  T& get(const vector<D, int>&);
-
-  vector<D, int> get_size() const;
-  void set_size(const vector<D, int>&);
-  void set_size(const int);
-  void initialize(const int i);
-};
-
-
-// grid_field
-// ~~~~~~~~~~~~
-template<int D, class T>
-grid_field<D, T>::grid_field()
-  : f(0), elements(0)
-{
-}
-
-
-// grid_field
-// ~~~~~~~~~~~~
-template<int D, class T>
-grid_field<D, T>::grid_field(const vector<D, int>& s)
-  : f(0)
-{
-  set_size(s);
-}
-
-
-// ~grid_field
-// ~~~~~~~~~~~~~
-template <int D, class T>
-grid_field<D, T>::~grid_field()
-{
-  if(f != 0)
-    delete[] f;
-}
-
-
-// get_size
-// ~~~~~~~~
-template<int D, class T>
-inline vector<D, int> grid_field<D, T>::get_size() const
-{
-  return size;
-}
-
-
-// set_size
-// ~~~~~~~~
-template<int D, class T>
-void grid_field<D, T>::set_size(const vector<D, int>& s)
-{
-  if(f != 0)
-    delete[] f;
-
-  size = s;
-
-  elements = 1;
-  for(int i=0; i<D; i++) {
-    offset[i] = elements;
-    elements *= size.x[i];
-  }
-
-  f = new T[elements];
-}
-
-
-// set_size
-// ~~~~~~~~
-template<int D, class T>
-void grid_field<D, T>::set_size(const int s)
-{
-  vector<D, int> square;
-
-  for(int k=0; k<D; k++)
-    square[k] = s;
-
-  set_size(square);
-}
-
-
-// get
-// ~~~
-template<int D, class T>
-inline T& grid_field<D, T>::get(const vector<D, int>& pos)
-{
-  int p=0;
-  for(int i=0; i<D; i++)
-    p += pos.x[i]*offset[i];
-
-  return f[p];
-}
-
-
-// initialize
-// ~~~
-template<int D, class T>
-void grid_field<D, T>::initialize(const int value)
-{
-  for(int i=0; i<elements; i++)
-    f[i] = value;
-}
-
-
-
-#endif
diff --git a/src/spheres_poly/heap.cpp b/src/spheres_poly/heap.cpp
deleted file mode 100644
index c83865c..0000000
--- a/src/spheres_poly/heap.cpp
+++ /dev/null
@@ -1,186 +0,0 @@
-#include "heap.h"
-#include "event.h"
-#include <iostream>
-#include "box.h"
-
-
-//==============================================================
-//==============================================================
-//  Class heap: Event heap used in hard spheres calculation
-//==============================================================
-//==============================================================
-
-
-//==============================================================
-// Constructor
-//==============================================================
-heap::heap(int maxsize_i):
-  maxsize(maxsize_i)
-{
-  a = new int[maxsize];
-  index = new int[maxsize];
-  
-  N = 0;   // current number of events in heap
-}
-
-
-//==============================================================
-// Constructor
-//==============================================================
-heap::heap(const heap &h)
-{
-  maxsize = h.maxsize;
-  a = h.a;
-  index = h.index;
-  N = h.N;                // current number of events in heap
-  s = h.s;
-}
-
-
-//==============================================================
-// Destructor
-//==============================================================
-heap::~heap()
-{
-  delete[] a;
-  delete[] index;
-}
-
-//==============================================================
-// Upheap
-//==============================================================
-void heap::upheap(int k)
-{
-  int i = a[k];
-
-  while ((k>1)&&(s[a[k/2]].nextevent.time > s[i].nextevent.time))
-    {
-      a[k] = a[k/2];
-      index[a[k/2]] = k;
-      k = k/2;
-    }
-  a[k] = i;
-  index[i] = k;
-}
-
-//==============================================================
-// Downheap
-//==============================================================
-void heap::downheap(int k)
-{
-  int j;
-  int i = a[k];
-  
-  while(k <= N/2)
-    {
-      j = k+k;
-      if ((j < N)&&(s[a[j]].nextevent.time > s[a[j+1]].nextevent.time))
-	j++;
-      if (s[i].nextevent.time <= s[a[j]].nextevent.time)
-	break;
-      a[k] = a[j];
-      index[a[j]] = k;
-      k = j;
-    }
-  a[k] = i;
-  index[i] = k;
-}
-
-//==============================================================
-// Insert
-//==============================================================
-void heap::insert(int i)
-{
-  if (N >= maxsize)
-    std::cout << "error, N >= maxsize, cannot insert another event" << std::endl;
-  else
-    {
-      N++;
-      a[N] = i;
-      index[i] = N;
-      upheap(N);
-    }  
-}
-
-
-//==============================================================
-// Extract max
-//==============================================================
-int heap::extractmax()
-{
-  return a[1];
-}
-
-/*
-//==============================================================
-// Replace
-//==============================================================
-void heap::replace(int i)
-{
-  a[1] = i;
-  s[i].nextevent = t;
-
-  if (!(e.time > s[a[1]].nextevent.time))
-    {
-      if (!(s[a[1]].nextevent.j == INF))// must be check i'm changing to coll. at same time
-	std::cout << "error replaced non check with earlier time" << std::endl;
-      a[1] = i;
-      index[i] = 1;
-    }
-  else
-    {    
-      a[0] = i;
-      downheap(0);
-    }
-}
-*/
-
-//==============================================================
-// Search
-//==============================================================
-int heap::search(int j)
-{
-  for (int k=1; k<=N; k++)
-    {
-      if (a[k] == j)
-	return k;
-    }
-  return -1;
-}
-
-/*
-//==============================================================
-// Change
-//==============================================================
-void heap::change(int i)
-{
-  int iindex = index[i];
-  
-  if (s[i].nextevent.time == s[a[iindex]].nextevent.time)  
-    std::cout << "error changing an event to an equal time" << std::endl;
-  else if (s[i].nextevent.time > s[a[iindex]].nextevent.time)
-    std::cout << "error changing an event to a greater time" << std::endl;
-
-  a[iindex] = i;
-  upheap(iindex);
-}
-*/
-
-//==============================================================
-// Print
-//==============================================================
-void heap::print()
-{
-  for (int k=1; k<=N; k++)
-    std::cout << k << " " << a[k] << " " << s[a[k]].nextevent.j << " " << s[a[k]].nextevent.time << std::endl;
-}
-
-
-//==============================================================
-// Check index array
-//==============================================================
-void heap::checkindex()
-{
-  for (int k=1; k<=N; k++)
-    std::cout << k << " " << a[k] << " " << index[a[k]] << std::endl;
-}
diff --git a/src/spheres_poly/heap.h b/src/spheres_poly/heap.h
deleted file mode 100644
index 91180e3..0000000
--- a/src/spheres_poly/heap.h
+++ /dev/null
@@ -1,42 +0,0 @@
-//---------------------------------------------------------------------------
-// Event heap maker
-//---------------------------------------------------------------------------
-
-#ifndef  HEAP_H
-#define  HEAP_H
-
-#include "event.h"
-#include "sphere.h"
-
-class heap {
-
- public:
-
-  // constructor and destructor
-  heap(int maxsize);
-  heap(const heap &h);
-  ~heap();
-
-  // variables
-  int maxsize;   // max allowed number of events
-  int N;         // current number of events
-  int *a;
-  sphere *s;
-  int *index;     // array of indices for each sphere
-  //event minevent;
-
-
-  // functions which operate on a binary heap
-  
-  void upheap(int k);
-  void downheap(int k);
-  void insert(int i);
-  void replace(int i);
-  int search(int j);
-  void change(int i); 
-  int extractmax();
-  void print();
-  void checkindex();
-  
-};
-#endif 
diff --git a/src/spheres_poly/neighbor.cpp b/src/spheres_poly/neighbor.cpp
deleted file mode 100644
index 920c099..0000000
--- a/src/spheres_poly/neighbor.cpp
+++ /dev/null
@@ -1,40 +0,0 @@
-#include "vector.h"
-#include <iostream>
-#include "box.h"
-
-
-//==============================================================
-//==============================================================
-//  Class neighbor
-//==============================================================
-//==============================================================
-
-neighbor::neighbor(int i_i)
- : i(i_i)
-{
-}
-
-
-//==============================================================
-//==============================================================
-//  Class collision
-//==============================================================
-//==============================================================
-
-collision::collision(int i_i, box *b_i)
-  : neighbor(i_i),
-    b(b_i)
-{
-  ctime = dblINF;
-  cpartner = i;
-}
-
-
-//==============================================================
-// Operation is finding the next collision from a given cell
-//==============================================================
-void collision::Operation(int j, vector<DIM, int>& pboffset)
-{
-  b->PredictCollision(i, j, pboffset, ctime, cpartner, cpartnerpboffset);
-}
-
diff --git a/src/spheres_poly/sphere.cpp b/src/spheres_poly/sphere.cpp
deleted file mode 100644
index 0fbbd68..0000000
--- a/src/spheres_poly/sphere.cpp
+++ /dev/null
@@ -1,66 +0,0 @@
-#include "box.h"
-#include <iostream>
-#include <math.h>
-#include <stdlib.h>
-#include <time.h>
-
-#include "vector.h"
-
-//==============================================================
-//==============================================================
-//  Class Sphere: 
-//==============================================================
-//==============================================================
-
-
-//==============================================================
-// Constructor
-//==============================================================
-sphere::sphere()
-{
-}
-
-
-//==============================================================
-// Constructor
-//==============================================================
-sphere::sphere(const sphere& s)
-{
-  i = s.i;
-  x = s.x;
-  v = s.v;
-  cell = s.cell;
-  lutime = s.lutime;
-  nextevent = s.nextevent;
-  nextcollision = s.nextcollision;
-  r = s.r;
-  gr = s.gr;
-  m = s.m;
-  species=s.species;
-}
-
-//==============================================================
-// Constructor
-//==============================================================
-sphere::sphere(int i_i, vector<DIM> x_i, vector<DIM, int> cell_i, 
-	       double lutime_i, double r_i, double gr_i, double m_i, int species_i):
-  i(i_i),
-  x(x_i),
-  cell(cell_i),
-  lutime(lutime_i),
-  r(r_i),
-  gr(gr_i),
-  m(m_i),
-  species(species_i)
-{
-}
-
-//==============================================================
-// Destructor
-//==============================================================
-sphere::~sphere() 
-{
-
-}
-
- 
diff --git a/src/spheres_poly/sphere.h b/src/spheres_poly/sphere.h
deleted file mode 100644
index 28c64b4..0000000
--- a/src/spheres_poly/sphere.h
+++ /dev/null
@@ -1,44 +0,0 @@
-#ifndef  SPHERE_H
-#define  SPHERE_H
-
-
-#include "vector.h"
-
-
-class sphere {
-
- public:
-
-  // constructor and destructor
-
-  sphere();
-  sphere(const sphere& s);
-  sphere(int i_i, vector<DIM> x, vector<DIM, int> cell_i, double lutime_i, 
-	 double r_i, double gr_i, double m_i, int species_i);
-  ~sphere();
-
- //variables
-  
-  int i;                          // sphere ID
-
-  // impending event
-  event nextevent;                // next event...can be collision or transfer
-  event nextcollision;            // next collision if next event is transfer
-  // maybe nextnext event
-  
-  // past information
-  double lutime;                  // last update time
-  vector<DIM, int> cell;          // cell that it belongs to
-  vector<DIM, double> x;          // position
-  vector<DIM, double> v;          // velocity
-  double r;                       // sphere radius
-  double gr;                      // sphere growth rate
-  double m;                       // sphere mass
-  int species;                    // species number (not used during the MD)
-  // make sure efficent in memory
-
- 
-
-};
-
-#endif 
diff --git a/src/spheres_poly/spheres.cpp b/src/spheres_poly/spheres.cpp
deleted file mode 100644
index 9b14b01..0000000
--- a/src/spheres_poly/spheres.cpp
+++ /dev/null
@@ -1,64 +0,0 @@
-//===========================================================
-//===========================================================
-//===========================================================
-//
-//  Molecular dynamics simulation of hardspheres
-//
-//===========================================================
-//===========================================================
-//===========================================================
-
-#include <iostream>
-#include <math.h>
-#include <fstream>
-#include <vector>
-#include <time.h>
-#include <string.h>
-#include <stdlib.h>
-#include <cstdlib>
-
-#include "box.h"
-#include "sphere.h"
-#include "event.h"
-#include "heap.h"
-
-
-double *spherespp(int N, double bidispersityratio, double bidispersityfraction, double maxpf, double maxpressure, double maxcollisionrate)
-{
-	int eventspercycle = 20;              // # events per sphere per cycle
-	double initialpf = 0.01;              // initial packing fraction
-	double temp = 0.2;                    // initial temp., use 0 for zero velocities
-	double growthrate = 0.001;            // growth rate
-	double massratio = 1.;               // ratio of sphere masses
-	int hardwallBC = 0;                   // 0 for periodic, 1 for hard wall BC
-
-  double d, r;   // initial diameter and radius of spheres
-
-  r = pow(initialpf*pow(SIZE, DIM)/(N*VOLUMESPHERE), 1.0/((double)(DIM)));
-
-  box b(N, r, growthrate, maxpf, bidispersityratio, 
-	bidispersityfraction, massratio, hardwallBC);
-
-	b.CreateSpheres(temp);
-  
-  
-  while ((b.collisionrate < maxcollisionrate) && (b.pf < maxpf) && (b.pressure < maxpressure)) 
-    {
-      b.Process(eventspercycle*N);
-      b.Synchronize(true);
-    }
-  
-	double *data = (double *)malloc(DIM * N * sizeof(double));
-
-  b.WriteConfiguration(data);
-  
-  return data;
-}
-
-extern "C" {
-	double *spheres(int N, double bidispersityratio, double bidispersityfraction, double maxpf, double maxpressure, double maxcollisionrate) {
-		return spherespp(N, bidispersityratio, bidispersityfraction, maxpf, maxpressure, maxcollisionrate);
-	}
-}
-
-
diff --git a/src/spheres_poly/spheres.h b/src/spheres_poly/spheres.h
deleted file mode 100644
index 44d8052..0000000
--- a/src/spheres_poly/spheres.h
+++ /dev/null
@@ -1,4 +0,0 @@
-
-#pragma once
-
-double *spheres(int N, double bidispersityratio, double bidispersityfraction, double maxpf, double maxpressure, double maxcollisionrate);
diff --git a/src/spheres_poly/vector.h b/src/spheres_poly/vector.h
deleted file mode 100644
index 9ee481f..0000000
--- a/src/spheres_poly/vector.h
+++ /dev/null
@@ -1,471 +0,0 @@
-#ifndef VECTOR_H
-#define VECTOR_H
-
-#include <iostream>
-#include <fstream>
-
-#define DIM 2
-
-template <int D, typename T=double>
-class vector {
-  
-  public:
-  T x[D];
-  
-  public:
-  
-  vector();
-  vector(const T[D]);           
-  vector(const vector&);
-  ~vector();
-
-  vector<D, T>& operator+=(const vector<D, T>&);
-  vector<D, T>& operator-=(const vector<D, T>&);
-  vector<D, T>& operator*=(const T);
-  vector<D, T>& operator/=(const T);
-  vector<D, T> operator+(const vector<D, T>&) const;
-  vector<D, T> operator-(const vector<D, T>&) const;
-  vector<D, T> operator*(const T) const;
-  vector<D, T> operator/(const T) const;
-  vector<D, T> operator%(const T) const;
-  bool operator==(const vector<D, T> &a) const;
-
-  vector<D, int> integer() const;
-  vector<D, double> Double() const;
-  static vector<D, int> integer(const vector<D, T>&); 
-  static vector<D, double> Double(const vector<D, T>&); 
-  
-  T& operator[](const unsigned int);
- 
-  double dot(const vector<D, T>&) const;
-  static double dot(const vector<D, T>&, const vector<D, T>&);
-  
-  double norm_squared() const;
-  static double norm_squared(const vector<D, T>&);
-
-  void read(std::ifstream&);
-  void write(std::ofstream&) const;
-};
-
-
-template <int D, typename T>
-std::ostream& operator<<(std::ostream&, const vector<D, T>&);
-
-
-// constructor
-// ~~~~~~~~~~~
-template <int D, typename T>
-vector<D, T>::vector()
-{
-  for(int k=0; k<D; k++)
-    x[k] = 0;
-}
-
-template <int D, typename T>
-vector<D, T>::vector(const T x_i[D])
-{
-  for(int k=0; k<D; k++)
-    x[k] = x_i[k];
-}
-
-template <int D, typename T>
-vector<D, T>::vector(const vector<D, T> &v)
-{
-  for(int k=0; k<D; k++)
-    x[k] = v.x[k];
-}
-
-
-// destructor
-// ~~~~~~~~~~
-template <int D, typename T>
-vector<D, T>::~vector()
-{
-}
-
-
-// +=
-// ~~
-template <int D, typename T>
-inline vector<D, T>& vector<D, T>::operator+=(const vector<D, T> &v)
-{
-  for(int k=0; k<D; k++)
-    x[k] += v.x[k];
-
-  return *this;
-}
-
-
-// -=
-// ~~
-template <int D, typename T>
-inline vector<D, T>& vector<D, T>::operator-=(const vector<D, T> &v)
-{
-  for(int k=0; k<D; k++)
-    x[k] -= v.x[k];
-
-  return *this;
-}
-
-
-// *=
-// ~~
-template <int D, typename T>
-inline vector<D, T>& vector<D, T>::operator*=(const T s)
-{
-  for(int k=0; k<D; k++)
-    x[k] *= s;
-
-  return *this;
-}
-
-// /=
-// ~~
-template <int D, typename T>
-inline vector<D, T>& vector<D, T>::operator/=(const T s)
-{
-  for(int k=0; k<D; k++)
-    x[k] /= s;
-
-  return *this;
-}
-
-
-// +
-// ~ 
-template <int D, typename T>
-inline vector<D, T> vector<D, T>::operator+(const vector<D, T> &a) const
-{
-  vector<D, T> c;
-  
-  for(int k=0; k<D; k++)
-    c.x[k] = x[k] + a.x[k];
-
-  return c;
-}
-
-
-// -
-// ~
-template <int D, typename T>
-inline vector<D, T> vector<D, T>::operator-(const vector<D, T> &a) const
-{
-  vector<D, T> c;
-
-  for(int k=0; k<D; k++)
-    c[k] = x[k] - a.x[k];
-
-  return c;
-}
-
-
-// *
-// ~
-template <int D, typename T>
-inline vector<D, T> vector<D, T>::operator*(const T s) const
-{
-  vector<D, T> c;
-  
-  for(int k=0; k<D; k++)
-    c[k] = x[k] * s;
-
-  return c;
-}
-
-
-// /
-// ~
-template <int D, typename T>
-inline vector<D, T> vector<D, T>::operator/(const T s) const
-{
-  vector<D, T> c;
-
-  for(int k=0; k<D; k++)
-    c[k] = x[k] / s;
-
-  return c;
-}
-
-
-// ==
-// ~
-template <int D, typename T>
-inline bool vector<D, T>::operator==(const vector<D, T> &a) const
-{
-  for(int k=0; k<D; k++)
-    {
-      if (!(x[k]==a.x[k]))
-	return false;
-    }
-  return true;
-}
-
-
-// %
-// ~
-template <int D, typename T>
-inline vector<D, T> vector<D, T>::operator%(const T s) const
-{
-  vector<D, T> c;
-
-  for(int k=0; k<D; k++)
-    c[k] = x[k] % s;
-
-  return c;
-}
-
-
-// integer
-// ~~~~~~~
-template <int D, typename T>
-inline vector<D, int> vector<D, T>::integer() const
-{
-  vector<D, int> c;
-
-  for(int k=0; k<D; k++)
-    c[k] = (int)x[k];
-
-  return c;
-}
-
-template <int D, typename T>
-inline vector<D, int> vector<D, T>::integer(const vector<D, T>& v)
-{
-  return v.integer();
-}
-
-
-// double
-// ~~~~~~~
-template <int D, typename T>
-inline vector<D, double> vector<D, T>::Double() const
-{
-  vector<D, double> c;
-
-  for(int k=0; k<D; k++)
-    c[k] = (double)x[k];
-
-  return c;
-}
-
-template <int D, typename T>
-inline vector<D, double> vector<D, T>::Double(const vector<D, T>& v)
-{
-  return v.Double();
-}
-
-
-
-// []
-// ~~
-template <int D, typename T>
-inline T& vector<D, T>::operator[](const unsigned int i)
-{
-  return x[i];
-}
-
-
-// Dot
-// ~~~
-template <int D, typename T>
-inline double vector<D, T>::dot(const vector<D, T> &a) const
-{
-  double d=0;
-
-  for(int k=0; k<D; k++)
-    d += x[k] * a.x[k];
-
-  return d;
-}
-
-template <int D, typename T>
-inline double vector<D, T>::dot(const vector<D, T> &a, const vector<D, T> &b)
-{
-  return a.dot(b);
-}
-
-
-// NormSquared
-// ~~~~~~~~~~~
-template <int D, typename T>
-inline double vector<D, T>::norm_squared() const
-{
-  return dot(*this, *this);
-}
-
-template <int D, typename T>
-inline double vector<D, T>::norm_squared(const vector<D, T>& v)
-{
-  return v.norm_squared();
-}
-
-
-// read
-// ~~~~
-template <int D, typename T>
-void vector<D, T>::read(std::ifstream& in)
-{
-  in.read((char*)x, sizeof(T)*D);
-}
-
-// write
-// ~~~~~
-template <int D, typename T>
-void vector<D, T>::write(std::ofstream& out) const
-{
-  out.write((const char*)x, sizeof(T)*D);
-}
-
-
-
-// Insertion
-// ~~~~~~~~~
-template <int D, typename T>
-std::ostream& operator<<(std::ostream& os, const vector<D, T>& v)
-{
-  os << "(";
-
-  for(int k=0; k<D-1; k++)
-    os << v.x[k] << ", ";
-
-  os << v.x[D-1] << ")";
-
-  return os;
-}
-
-
-// ======================================================================
-// vector_field 
-// ======================================================================
-
-// A field of V-vectors on a D dimensional manifold
-
-template<int V, int D, typename T=double>
-class vector_field {
-  
- public:
-  int elements;
-
- private:
-  vector<V, T>* f;
-  vector<D, int> size;           // number of grid points for each dimension
-  vector<D, int> offset;
- 
- public:
-
-  vector_field();
-  vector_field(const vector<D, int>&);
-  ~vector_field();
-
-  vector<D, int> get_size() const;
-  void set_size(const vector<D, int>&);
-
-  vector<V, T>& get(const vector<D, int>&);
-
-  void read(std::ifstream&);
-  void write(std::ofstream&) const;
-
-  static void swap(vector_field<V, D, T>&, vector_field<V, D, T>&);
-};
-
-
-// vector_field
-// ~~~~~~~~~~~~
-template<int V, int D, typename T>
-vector_field<V, D, T>::vector_field()
-  : f(0), elements(0)
-{
-}
-
-
-// vector_field
-// ~~~~~~~~~~~~
-template<int V, int D, typename T>
-vector_field<V, D, T>::vector_field(const vector<D, int>& s)
-  : f(0)
-{
-  set_size(s);
-}
-
-// ~vector_field
-// ~~~~~~~~~~~~~
-template <int V, int D, typename T>
-vector_field<V, D, T>::~vector_field()
-{
-  if(f != 0)
-    delete[] f;
-}
-
-// get_size
-// ~~~~~~~~
-template<int V, int D, typename T>
-inline vector<D, int> vector_field<V, D, T>::get_size() const
-{
-  return size;
-}
-
-// set_size
-// ~~~~~~~~
-template<int V, int D, typename T>
-void vector_field<V, D, T>::set_size(const vector<D, int>& s)
-{
-  if(f != 0)
-    delete[] f;
-
-  size = s;
-
-  elements = 1;
-  for(int i=0; i<D; i++) {
-    offset[i] = elements;
-    elements *= size.x[i];
-  }
-
-  f = new vector<V, T>[elements];
-}
-
-// get
-// ~~~
-template<int V, int D, typename T>
-inline vector<V, T>& vector_field<V, D, T>::get(const vector<D, int>& pos)
-{
-  int p=0;
-  for(int i=0; i<D; i++)
-    p += pos.x[i]*offset[i];
-
-  return f[p];
-}
-
-
-// read
-// ~~~~
-template<int V, int D, typename T>
-void vector_field<V, D, T>::read(std::ifstream& in)
-{
-  in.read((char*)f, elements*sizeof(T)*V);
-}
-
-
-// write
-// ~~~~~
-template<int V, int D, typename T>
-void vector_field<V, D, T>::write(std::ofstream& out) const
-{
-  out.write((const char*)f, elements*sizeof(T)*V);
-}
-
-// swap
-// ~~~~
-template<int V, int D, typename T>
-void vector_field<V, D, T>::swap(vector_field<V, D, T>& v1,
-				 vector_field<V, D, T>& v2)
-{
-  vector<V, T>* f;
-
-  f = v1.f;
-  v1.f = v2.f;
-  v2.f = f;
-}
-
-
-
-#endif