From a79c2f04682c44275d2415d39e6996802c4a83c4 Mon Sep 17 00:00:00 2001
From: Jaron Kent-Dobias <jkentdobias@g.hmc.edu>
Date: Thu, 1 May 2014 16:01:48 -0700
Subject: created a git repository for my thesis code.

---
 src/domain_improve.cpp | 145 +++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 145 insertions(+)
 create mode 100644 src/domain_improve.cpp

(limited to 'src/domain_improve.cpp')

diff --git a/src/domain_improve.cpp b/src/domain_improve.cpp
new file mode 100644
index 0000000..f69e85f
--- /dev/null
+++ b/src/domain_improve.cpp
@@ -0,0 +1,145 @@
+/* domain_improve.cpp
+ *
+ * Copyright (C) 2013 Jaron Kent-Dobias
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+/* A program which facilitates automated mapping of bifurcation points in the
+ * energy of a system where the Hessian is available.  Currently, only a one
+ * dimensional parameter space is supported.
+ */
+
+#include "domain_energy.h"
+#include "domain_minimize.h"
+#include "domain_eigen.h"
+
+#include <unistd.h>
+#include <stdio.h>
+#include <iostream>
+#include <stdlib.h>
+#include <math.h>
+#include <string>
+
+// GSL includes.
+#include <gsl/gsl_sf.h>
+#include <gsl/gsl_math.h>
+#include <gsl/gsl_complex.h>
+#include <gsl/gsl_complex_math.h>
+#include <gsl/gsl_vector.h>
+#include <gsl/gsl_permutation.h>
+#include <gsl/gsl_permute_vector.h>
+#include <gsl/gsl_blas.h>
+#include <gsl/gsl_linalg.h>
+#include <gsl/gsl_sort_vector.h>
+
+
+// Initializes the program.
+int main(int argc, char *argv[]) {
+
+	int opt, min_fails;
+	unsigned n, N, num;
+	double c, g0, g, eps, energy;
+	char *filename;
+	bool eigenpres = true;
+
+	// Setting default values.
+	eps = 0;
+	num = 25;
+
+	gsl_vector *z, *old_z, *eigenvalues, *trueEigenvalues;
+	gsl_permutation *eigenorder, *trueEigenorder;
+
+	while ((opt = getopt(argc, argv, "n:c:d:g:h:i:N:p:m:j:e:t:s")) != -1) {
+		switch (opt) {
+			case 'n':
+				n = atoi(optarg);
+				break;
+			case 'N':
+				N = atoi(optarg);
+				break;
+			case 'g':
+				g0 = atof(optarg);
+				break;
+			case 'i':
+				filename = optarg;
+				break;
+			case 'e':
+				eps = atof(optarg);
+				break;
+			default:
+				exit(EXIT_FAILURE);
+		}
+	}
+
+	z = gsl_vector_alloc(3 * n + 3);
+	old_z = gsl_vector_alloc(3 * n + 3);
+	eigenvalues = gsl_vector_alloc(3 * n + 3);
+	trueEigenvalues = gsl_vector_alloc(3 * n + 4);
+	eigenorder = gsl_permutation_alloc(3 * n + 3);
+	trueEigenorder = gsl_permutation_alloc(3 * n + 4);
+
+	g = g0;
+
+	char ch;
+	double throwaway;
+
+	FILE *f = fopen(filename, "r+");
+	while (ch != '\n') ch = fgetc(f);
+	ch = 'a';
+	while (ch != '\n' && ch != '\t') ch = fgetc(f);
+	if (ch == '\n') eigenpres = false;
+
+	rewind(f);
+
+	fscanf(f, "%le\t", &c);
+	fscanf(f, "%le\n", &energy);
+
+	if (eigenpres) {
+		ch = 'a';
+		while (ch != '\n') ch = fgetc(f);
+	}
+	gsl_vector_fscanf(f, z);
+	fclose(f);
+
+	min_fails = domain_minimize_fixed(z, n, c, eps, g, N, 4, 2);
+
+	if (min_fails) {
+		printf("BIFUR: Initial relaxation failed, exiting.\n");
+		return 1;
+	}
+
+//	domain_eigen_values(eigenvalues, n, z, c);
+//	domain_eigen_sort(eigenorder, n, num, eigenvalues);
+
+	energy = domain_energy_fixedEnergy(n, z, c);
+	unsigned ii;
+
+	FILE *newf = fopen(filename, "w");
+	fprintf(newf, "%.12le\t%.12le\n", c, energy);
+	for (unsigned i = 0; i < num; i++) {
+		ii = gsl_permutation_get(eigenorder, i);
+		fprintf(newf, "%.12le\t", gsl_vector_get(eigenvalues, ii));
+	}
+	fprintf(newf, "\n");
+	for (unsigned i = 0; i < num; i++) {
+		ii = gsl_permutation_get(trueEigenorder, i);
+		fprintf(newf, "%.12le\t", gsl_vector_get(trueEigenvalues, ii));
+	}
+	fprintf(newf, "\n");
+	for (unsigned i = 0; i < 3 * n + 3; i++) {
+		fprintf(newf, "%.12le\t", gsl_vector_get(z, i));
+	}
+	fclose(newf);
+}
-- 
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