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update to WHAM version 2.1.0

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This commit is contained in:
Axel Kohlmeyer
2025-03-16 17:25:55 -04:00
parent 035aefcc26
commit d65b0ce666
2 changed files with 62 additions and 310 deletions
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514
tools/lammps-gui/update-wham-2.1.0.patch Normal file
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@ -0,0 +1,514 @@
diff --git a/CMakeLists.txt b/CMakeLists.txt
index b4f0fe6..a61cec8 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,7 +1,7 @@
# Custom minimal -*- CMake -*- file for wham
cmake_minimum_required(VERSION 3.16)
-project(wham VERSION 2.0.11
+project(wham VERSION 2.1.0
DESCRIPTION "WHAM: a fast, memory efficient implementation of the Weighted Histogram Analysis Method"
LANGUAGES C
HOMEPAGE_URL http://membrane.urmc.rochester.edu/content/wham/)
diff --git a/doc/doc.tex b/doc/doc.tex
index cf36616..84ee891 100644
--- a/doc/doc.tex
+++ b/doc/doc.tex
@@ -53,7 +53,7 @@ Suggestions and patches are welcome.
\subsection{New in release 2.1.0}
-Two changes, both contributed by Alex Kohlmeyer. First, we switched from old
+Two changes, both contributed by Axel Kohlmeyer. First, we switched from old
make to CMake for the build. Second, we changed how energy units are set; where
it used to be a compile-time option, now it is set on the command line.
diff --git a/wham-2d/histogram.c b/wham-2d/histogram.c
index 1bd1329..b5d1c01 100644
--- a/wham-2d/histogram.c
+++ b/wham-2d/histogram.c
@@ -78,14 +78,14 @@ return hp;
}
/* Get a value from a histogram structure
- * Given i and j, the indices into the global histogram, return
+ * Given i and j, the indices into the global histogram, return
* the correct histogram value. Since we only store range of histogram
- * indices containing the nonzero values, we have to check the index value
+ * indices containing the nonzero values, we have to check the index value
* against the range in the structure.
*/
double get_histval(struct histogram *hist, int i, int j)
{
-if ( (i < hist->first_x) || (i > hist->last_x)
+if ( (i < hist->first_x) || (i > hist->last_x)
||(j < hist->first_y) || (j > hist->last_y))
{
return 0.0;
@@ -239,7 +239,7 @@ return error;
// Calculate the free energy, setting the minimum value to 0
-void calc_free(double **free, double **prob, double kT,
+void calc_free(double **free, double **prob, double kT,
int use_mask, int **mask)
{
int i,j;
@@ -257,7 +257,14 @@ for (i=0; i<NUM_BINSx; i++)
}
else
{
- free[i][j] = -kT * log(prob[i][j]);
+ if (prob[i][j] > 0.0)
+ {
+ free[i][j] = -kT * log(prob[i][j]);
+ }
+ else
+ {
+ free[i][j] = 0.0;
+ }
if (free[i][j] < min)
{
min = free[i][j];
@@ -321,8 +328,6 @@ return 0.5*(springx*(dx*dx) + springy*(dy*dy));
void calc_coor(int i, int j, double *coor)
{
-coor[0] = HIST_MINx + BIN_WIDTHx*((double)i+0.5);
-coor[1] = HIST_MINy + BIN_WIDTHy*((double)j+0.5);
+coor[0] = HIST_MINx + BIN_WIDTHx*((double)i+0.5);
+coor[1] = HIST_MINy + BIN_WIDTHy*((double)j+0.5);
}
-
-
diff --git a/wham-2d/wham-2d.c b/wham-2d/wham-2d.c
index 76389ac..05fe7cf 100644
--- a/wham-2d/wham-2d.c
+++ b/wham-2d/wham-2d.c
@@ -417,8 +417,8 @@ while ( ! iConverged || first)
for (j=0; j< NUM_BINSy; j++)
{
calc_coor(i,j,coor);
- printf("%f\t%f\t%f\t%f\n", coor[0], coor[1], free_ene[i][j],
- prob[i][j]);
+ if (prob[i][j] != 0.0)
+ printf("%f\t%f\t%f\t%f\n", coor[0], coor[1], free_ene[i][j], prob[i][j]);
}
}
@@ -501,8 +501,9 @@ if (!FREEFILE)
for (j=0; j< NUM_BINSy; j++)
{
calc_coor(i,j,coor);
- printf("%f\t%f\t%f\t%f\n", coor[0], coor[1],
- free_ene[i][j], final_prob[i][j]);
+ if (prob[i][j] != 0.0)
+ printf("%f\t%f\t%f\t%f\n", coor[0], coor[1],
+ free_ene[i][j], final_prob[i][j]);
}
}
exit(errno);
@@ -518,25 +519,28 @@ else
for (j=-numpad; j<0; j++)
{
calc_coor(i,j,coor);
- fprintf(FREEFILE,"%f\t%f\t%f\t%f\n", coor[0], coor[1],
- free_ene[NUM_BINSx+i][NUM_BINSy+j],
- final_prob[NUM_BINSx+i][NUM_BINSy+j]);
+ if (prob[NUM_BINSx+i][NUM_BINSy+j] != 0.0)
+ fprintf(FREEFILE,"%f\t%f\t%f\t%f\n", coor[0], coor[1],
+ free_ene[NUM_BINSx+i][NUM_BINSy+j],
+ final_prob[NUM_BINSx+i][NUM_BINSy+j]);
}
// center values in y
for (j=0; j<NUM_BINSy; j++)
{
calc_coor(i,j,coor);
- fprintf(FREEFILE,"%f\t%f\t%f\t%f\n", coor[0], coor[1],
- free_ene[NUM_BINSx+i][j],
- final_prob[NUM_BINSx+i][j]);
+ if (prob[NUM_BINSx+i][j] != 0.0)
+ fprintf(FREEFILE,"%f\t%f\t%f\t%f\n", coor[0], coor[1],
+ free_ene[NUM_BINSx+i][j],
+ final_prob[NUM_BINSx+i][j]);
}
// trailing padding values in y
for (j=0; j<numpad; j++)
{
calc_coor(i,NUM_BINSy+j,coor);
- fprintf(FREEFILE,"%f\t%f\t%f\t%f\n", coor[0], coor[1],
- free_ene[NUM_BINSx+i][j],
- final_prob[NUM_BINSx+i][j]);
+ if (prob[NUM_BINSx+i][j] != 0.0)
+ fprintf(FREEFILE,"%f\t%f\t%f\t%f\n", coor[0], coor[1],
+ free_ene[NUM_BINSx+i][j],
+ final_prob[NUM_BINSx+i][j]);
}
fprintf(FREEFILE, "\n");
}
@@ -547,25 +551,28 @@ else
for (j=-numpad; j<0; j++)
{
calc_coor(i,j,coor);
- fprintf(FREEFILE,"%f\t%f\t%f\t%f\n", coor[0], coor[1],
- free_ene[i][NUM_BINSy+j],
- final_prob[i][NUM_BINSy+j]);
+ if (prob[i][NUM_BINSy+j] != 0.0)
+ fprintf(FREEFILE,"%f\t%f\t%f\t%f\n", coor[0], coor[1],
+ free_ene[i][NUM_BINSy+j],
+ final_prob[i][NUM_BINSy+j]);
}
// center values in y
for (j=0; j<NUM_BINSy; j++)
{
calc_coor(i,j,coor);
- fprintf(FREEFILE,"%f\t%f\t%f\t%f\n", coor[0], coor[1],
- free_ene[i][j],
- final_prob[i][j]);
+ if (prob[i][j] != 0.0)
+ fprintf(FREEFILE,"%f\t%f\t%f\t%f\n", coor[0], coor[1],
+ free_ene[i][j],
+ final_prob[i][j]);
}
// trailing padding values in y
for (j=0; j<numpad; j++)
{
calc_coor(i,NUM_BINSy+j,coor);
- fprintf(FREEFILE,"%f\t%f\t%f\t%f\n", coor[0], coor[1],
- free_ene[i][j],
- final_prob[i][j]);
+ if (prob[i][j] != 0.0)
+ fprintf(FREEFILE,"%f\t%f\t%f\t%f\n", coor[0], coor[1],
+ free_ene[i][j],
+ final_prob[i][j]);
}
fprintf(FREEFILE, "\n");
}
@@ -576,25 +583,28 @@ else
for (j=-numpad; j<0; j++)
{
calc_coor(NUM_BINSx+i,j,coor);
- fprintf(FREEFILE,"%f\t%f\t%f\t%f\n", coor[0], coor[1],
- free_ene[i][NUM_BINSy+j],
- final_prob[i][NUM_BINSy+j]);
+ if (prob[i][NUM_BINSy+j] != 0.0)
+ fprintf(FREEFILE,"%f\t%f\t%f\t%f\n", coor[0], coor[1],
+ free_ene[i][NUM_BINSy+j],
+ final_prob[i][NUM_BINSy+j]);
}
// center values in y
for (j=0; j<NUM_BINSy; j++)
{
calc_coor(NUM_BINSx+i,j,coor);
- fprintf(FREEFILE,"%f\t%f\t%f\t%f\n", coor[0], coor[1],
- free_ene[i][j],
- final_prob[i][j]);
+ if (prob[i][j] != 0.0)
+ fprintf(FREEFILE,"%f\t%f\t%f\t%f\n", coor[0], coor[1],
+ free_ene[i][j],
+ final_prob[i][j]);
}
// trailing padding values in y
for (j=0; j<numpad; j++)
{
calc_coor(NUM_BINSx+i,NUM_BINSy+j,coor);
- fprintf(FREEFILE,"%f\t%f\t%f\t%f\n", coor[0], coor[1],
- free_ene[i][j],
- final_prob[i][j]);
+ if (prob[i][j] != 0.0)
+ fprintf(FREEFILE,"%f\t%f\t%f\t%f\n", coor[0], coor[1],
+ free_ene[i][j],
+ final_prob[i][j]);
}
fprintf(FREEFILE, "\n");
}
diff --git a/wham/histogram.c b/wham/histogram.c
index bc52d74..635b39f 100644
--- a/wham/histogram.c
+++ b/wham/histogram.c
@@ -16,7 +16,7 @@
// Allocate memory for a histogram
-struct histogram *hist_alloc(int first, int last, int num_points,
+struct histogram *hist_alloc(int first, int last, int num_points,
int num_mc_samples)
{
struct histogram *hp;
@@ -45,9 +45,9 @@ return hp;
}
/* Get a value from a histogram structure
- * Given index, the index into the global histogram, return
+ * Given index, the index into the global histogram, return
* the correct histogram value. Since we only store range of histogram
- * indices containing the nonzero values, we have to check the index value
+ * indices containing the nonzero values, we have to check the index value
* against the range in the structure.
*/
double get_histval(struct histogram *hist, int index)
@@ -213,8 +213,16 @@ double min = 1e50;
bin_min = 0;
for (i=0; i<NUM_BINS; i++)
{
- free[i] = -kT * log(prob[i]);
- if (free[i] < min)
+ if (prob[i] > 0.0)
+ {
+ free[i] = -kT * log(prob[i]);
+ }
+ else
+ {
+ free[i] = 0.0;
+ }
+
+ if (free[i] < min)
{
min = free[i];
bin_min = i;
@@ -252,5 +260,5 @@ return 0.5*dx*dx*spring;
double calc_coor(int i)
{
-return HIST_MIN + BIN_WIDTH*((double)i+0.5);
+return HIST_MIN + BIN_WIDTH*((double)i+0.5);
}
diff --git a/wham/wham.c b/wham/wham.c
index 19cf695..7bdbce1 100644
--- a/wham/wham.c
+++ b/wham/wham.c
@@ -1,4 +1,4 @@
-/*
+/*
* WHAM -- Weighted Histogram Analysis Method
*
* Reference 1: Computer Physics Communications, 91(1995) 275-282, Benoit Roux
@@ -39,10 +39,9 @@ double kT; // temperature
int i,j;
int len;
int first;
-int bin_min;
int have_energy;
char *freefile;
-FILE *METAFILE, *FREEFILE;
+FILE *METAFILE, *FREEFILE;
struct hist_group *hist_group;
struct histogram *hp;
double coor;
@@ -179,7 +178,7 @@ if (argc != 9 && argc !=11)
printf( COMMAND_LINE );
exit(-1);
}
-
+
HIST_MIN = atof(argv[1]);
HIST_MAX = atof(argv[2]);
NUM_BINS = atoi(argv[3]);
@@ -269,13 +268,13 @@ if (!ave_pdf2)
printf("couldn't allocate space for ave_pdf2: %s\n", strerror(errno));
exit(errno);
}
-
+
free_ene = (double *) malloc(sizeof(double) * NUM_BINS);
if (!free_ene)
{
printf("couldn't allocate space for free_ene: %s\n", strerror(errno));
exit(errno);
- }
+ }
i = get_numwindows(METAFILE);
printf("#Number of windows = %d\n", i);
@@ -304,7 +303,7 @@ assert(i == hist_group->num_windows);
// Figure out if we have trajectories at different temperatures.
// Missing temperatures are set to -1 in read_metadata, and
// since we require that either all trajectories specify a temperature
-// or all trajectories are assumed to be at the wham temperature, we only
+// or all trajectories are assumed to be at the wham temperature, we only
// have to check one of them
if (hist_group->kT[0] > 0)
{
@@ -313,7 +312,7 @@ if (hist_group->kT[0] > 0)
else
{
have_energy = 0;
- for (i=0; i< hist_group->num_windows; i++)
+ for (i=0; i< hist_group->num_windows; i++)
{
hist_group->kT[i] = kT;
}
@@ -325,7 +324,7 @@ if (!final_f)
{
printf("couldn't allocate space for final_f: %s\n", strerror(errno));
exit(errno);
- }
+ }
free(HISTOGRAM);
@@ -361,7 +360,8 @@ while (! is_converged(hist_group) || first )
for (i=0; i< NUM_BINS; i++)
{
coor = calc_coor(i);
- printf("%f\t%f\t%f\n", coor, free_ene[i], prob[i]);
+ if (prob[i] != 0.0)
+ printf("%f\t%f\t%f\n", coor, free_ene[i], prob[i]);
}
printf("\n");
@@ -375,7 +375,7 @@ while (! is_converged(hist_group) || first )
}
}
// Cheesy bailout if we're going on too long
- if (iteration >= max_iteration)
+ if (iteration >= max_iteration)
{
printf("Too many iterations: %d\n", iteration);
break;
@@ -408,7 +408,7 @@ for (i=0; i < NUM_BINS; i++)
}
// Compute the free energy from the normalized probability
-bin_min = calc_free(free_ene, prob,kT);
+ calc_free(free_ene, prob,kT);
// Do the requested number of bootstrap monte carlo error analysis runs.
if (num_mc_runs <= 0)
@@ -439,11 +439,11 @@ for (i=0; i< num_mc_runs; i++)
//printf("Faking %d: %d %d\n", i,j,hp->num_points);
num_used = hp->last - hp->first + 1;
mk_new_hist(hp->cum, hp->data, num_used, hp->num_mc_samples, &idum);
-
+
hist_group->F_old[j] = 0.0;
hist_group->F[j] = 0.0;
}
-
+
// perform WHAM iterations on the fake data sets
iteration = 0;
first = 1;
@@ -459,7 +459,7 @@ for (i=0; i< num_mc_runs; i++)
printf("Too many iterations: %d\n", iteration);
break;
}
- }
+ }
printf("#MC trial %d: %d iterations\n", i, iteration);
printf("#PMF values\n");
// accumulate the average and stdev of the resulting probabilities
@@ -475,18 +475,19 @@ for (i=0; i< num_mc_runs; i++)
for (j=0; j < NUM_BINS; j++)
{
pdf = -kT*log(prob[j]);
-
+
ave_p[j] += prob[j];
ave_pdf[j] += pdf;
ave_p2[j] += prob[j] * prob[j];
ave_pdf2[j] += pdf*pdf;
}
- for (j=0; j<hist_group->num_windows;j++)
+ for (j=0; j<hist_group->num_windows;j++)
{
ave_F[j] += hist_group->F[j] - hist_group->F[0];
- ave_F2[j] += hist_group->F[j]*hist_group->F[j] ;
+ ave_F2[j] += hist_group->F[j]*hist_group->F[j] ;
}
- }
+ }
+ if (num_mc_runs == 0) num_mc_runs = 1;
for (i=0; i < NUM_BINS; i++)
{
ave_p[i] /= (double)num_mc_runs;
@@ -513,12 +514,12 @@ if (!FREEFILE)
for (i=0; i< NUM_BINS; i++)
{
coor = calc_coor(i);
- printf("%f\t%f\t%f\t%f\t%f\n", coor, free_ene[i], ave_pdf2[i],
- prob[i], ave_p2[i]);
+ if (prob[i] != 0.0)
+ printf("%f\t%f\t%f\t%f\t%f\n", coor, free_ene[i], ave_pdf2[i], prob[i], ave_p2[i]);
}
for (i=0; i<hist_group->num_windows; i++)
{
- fprintf(FREEFILE,"%d\t%f\t%f\n", i, final_f[i],ave_F2[i]);
+ printf("%d\t%f\t%f\n", i, final_f[i],ave_F2[i]);
}
exit(errno);
@@ -526,38 +527,37 @@ if (!FREEFILE)
else
{
// write out header
- fprintf(FREEFILE, "#Coor\t\tFree\t+/-\t\tProb\t\t+/-\n");
+ fprintf(FREEFILE, "#Coor\t\tFree\t\t+/-\t\tProb\t\t+/-\n");
// write out the leading padded values
for (i=-numpad; i<0; i++)
{
coor = calc_coor(i);
- fprintf(FREEFILE,"%f\t%f\t%f\t%f\t%f\n", coor, free_ene[NUM_BINS+i],
- ave_pdf2[NUM_BINS+i],
- final_prob[NUM_BINS+i],
- ave_p2[NUM_BINS+i]);
+ if (prob[NUM_BINS+1] != 0.0)
+ fprintf(FREEFILE,"%f\t%f\t%f\t%f\t%f\n", coor, free_ene[NUM_BINS+i],
+ ave_pdf2[NUM_BINS+i], final_prob[NUM_BINS+i], ave_p2[NUM_BINS+i]);
}
// write out the center values
for (i=0; i<NUM_BINS; i++)
{
coor = calc_coor(i);
- fprintf(FREEFILE,"%f\t%f\t%f\t%f\t%f\n", coor, free_ene[i],
- ave_pdf2[i],final_prob[i],
- ave_p2[i]);
+ if (prob[i] != 0.0)
+ fprintf(FREEFILE,"%f\t%f\t%f\t%f\t%f\n", coor, free_ene[i],
+ ave_pdf2[i],final_prob[i],ave_p2[i]);
}
// write out the trailing padded values
for (i=0; i<numpad; i++)
{
coor = calc_coor(NUM_BINS+i);
- fprintf(FREEFILE,"%f\t%f\t%f\t%f\t%f\n", coor, free_ene[i],
- ave_pdf2[i],final_prob[i],
- ave_p2[i]);
+ if (prob[i] != 0.0)
+ fprintf(FREEFILE,"%f\t%f\t%f\t%f\t%f\n", coor, free_ene[i],
+ ave_pdf2[i],final_prob[i], ave_p2[i]);
}
- fprintf(FREEFILE, "#Window\t\tFree\t+/-\t\n");
+ fprintf(FREEFILE, "#Window\t\tFree\t\t+/-\t\n");
for (i=0; i<hist_group->num_windows; i++)
{
- fprintf(FREEFILE,"#%d\t%f\t%f\n", i, final_f[i],ave_F2[i]);
+ fprintf(FREEFILE,"#%d\t\t%f\t%f\n", i, final_f[i],ave_F2[i]);
}
}
@@ -571,7 +571,7 @@ exit(0);
/*
* Perform a single WHAM iteration
*/
-void wham_iteration(struct hist_group* hist_group, double *prob,
+void wham_iteration(struct hist_group* hist_group, double *prob,
int have_energy)
{
int i,j;
@@ -591,9 +591,9 @@ for (i=0; i<NUM_BINS; i++)
num += (double) get_histval( &(hist_group->hists[j]),i);
bias = calc_bias(hist_group,j,coor);
bf = exp((hist_group->F_old[j] - bias) / hist_group->kT[j]);
- /* If we have energies, then the histograms contain boltzmann
- * factors. If not, they contain integer counts. Accordingly,
- * we either use a partition function to normalize, or simply the
+ /* If we have energies, then the histograms contain boltzmann
+ * factors. If not, they contain integer counts. Accordingly,
+ * we either use a partition function to normalize, or simply the
* number of points.
*/
if (have_energy)