int main(int argc, const char *argv[]) {
took("Starting program");
// ----------------------------------------------------------------------------
// Define "Constants" -- set from arguments then unchanged
// ----------------------------------------------------------------------------
// NOTE: debug can slow things down VERY much
int debug = false;
int test_weights = false;
int print_weights = false;
int no_weights = false;
double fix_kT = 0;
int flat_histogram = false;
int gaussian_fit = false;
int walker_weights = false;
int wang_landau = false;
double wl_factor = 0.125;
double wl_fmod = 2;
double wl_threshold = 0.1;
double wl_cutoff = 1e-6;
sw_simulation sw;
sw.len[0] = sw.len[1] = sw.len[2] = 1;
sw.walls = 0;
int wall_dim = 1;
unsigned long int seed = 0;
char *dir = new char[1024];
sprintf(dir, "papers/square-well-liquid/data");
char *filename = new char[1024];
sprintf(filename, "default_filename");
sw.N = 1000;
long iterations = 2500000;
long initialization_iterations = 500000;
double acceptance_goal = .4;
double R = 1;
double well_width = 1.3;
double ff = 0.3;
double neighbor_scale = 2;
sw.dr = 0.1;
double de_density = 0.1;
double de_g = 0.05;
double max_rdf_radius = 10;
int totime = 0;
// scale is not a quite "constant" -- it is adjusted during the initialization
// so that we have a reasonable acceptance rate
double translation_scale = 0.05;
poptContext optCon;
// ----------------------------------------------------------------------------
// Set values from parameters
// ----------------------------------------------------------------------------
poptOption optionsTable[] = {
{"N", '\0', POPT_ARG_INT, &sw.N, 0, "Number of balls to simulate", "INT"},
{"ww", '\0', POPT_ARG_DOUBLE | POPT_ARGFLAG_SHOW_DEFAULT, &well_width, 0,
"Ratio of square well width to ball diameter", "DOUBLE"},
{"ff", '\0', POPT_ARG_DOUBLE, &ff, 0, "Filling fraction. If specified, the "
"cell dimensions are adjusted accordingly without changing the shape of "
"the cell"},
{"walls", '\0', POPT_ARG_INT | POPT_ARGFLAG_SHOW_DEFAULT, &sw.walls, 0,
"Number of walled dimensions (dimension order: x,y,z)", "INT"},
{"initialize", '\0', POPT_ARG_LONG | POPT_ARGFLAG_SHOW_DEFAULT,
&initialization_iterations, 0,
"Number of iterations to run for initialization", "INT"},
{"iterations", '\0', POPT_ARG_LONG | POPT_ARGFLAG_SHOW_DEFAULT, &iterations,
0, "Number of iterations to run for", "INT"},
{"de_g", '\0', POPT_ARG_DOUBLE | POPT_ARGFLAG_SHOW_DEFAULT, &de_g, 0,
"Resolution of distribution functions", "DOUBLE"},
{"dr", '\0', POPT_ARG_DOUBLE | POPT_ARGFLAG_SHOW_DEFAULT, &sw.dr, 0,
"Differential radius change used in pressure calculation", "DOUBLE"},
{"de_density", '\0', POPT_ARG_DOUBLE | POPT_ARGFLAG_SHOW_DEFAULT,
&de_density, 0, "Resolution of density file", "DOUBLE"},
{"max_rdf_radius", '\0', POPT_ARG_DOUBLE | POPT_ARGFLAG_SHOW_DEFAULT,
&max_rdf_radius, 0, "Set maximum radius for RDF data collection", "DOUBLE"},
{"lenx", '\0', POPT_ARG_DOUBLE, &sw.len[x], 0,
"Relative cell size in x dimension", "DOUBLE"},
{"leny", '\0', POPT_ARG_DOUBLE, &sw.len[y], 0,
"Relative cell size in y dimension", "DOUBLE"},
{"lenz", '\0', POPT_ARG_DOUBLE, &sw.len[z], 0,
"Relative cell size in z dimension", "DOUBLE"},
{"filename", '\0', POPT_ARG_STRING | POPT_ARGFLAG_SHOW_DEFAULT, &filename, 0,
"Base of output file names", "STRING"},
{"dir", '\0', POPT_ARG_STRING | POPT_ARGFLAG_SHOW_DEFAULT, &dir, 0,
"Save directory", "dir"},
{"neighbor_scale", '\0', POPT_ARG_DOUBLE | POPT_ARGFLAG_SHOW_DEFAULT,
&neighbor_scale, 0, "Ratio of neighbor sphere radius to interaction scale "
"times ball radius. Drastically reduces collision detections","DOUBLE"},
{"translation_scale", '\0', POPT_ARG_DOUBLE | POPT_ARGFLAG_SHOW_DEFAULT,
&translation_scale, 0, "Standard deviation for translations of balls, "
"relative to ball radius", "DOUBLE"},
{"seed", '\0', POPT_ARG_INT | POPT_ARGFLAG_SHOW_DEFAULT, &seed, 0,
"Seed for the random number generator", "INT"},
{"acceptance_goal", '\0', POPT_ARG_DOUBLE | POPT_ARGFLAG_SHOW_DEFAULT,
&acceptance_goal, 0, "Goal to set the acceptance rate", "DOUBLE"},
{"nw", '\0', POPT_ARG_NONE, &no_weights, 0, "Don't use weighing method "
"to get better statistics on low entropy states", "BOOLEAN"},
{"kT", '\0', POPT_ARG_DOUBLE, &fix_kT, 0, "Use a fixed temperature of kT"
" rather than adjusted weights", "DOUBLE"},
{"flat", '\0', POPT_ARG_NONE, &flat_histogram, 0,
"Use a flat histogram method", "BOOLEAN"},
{"gaussian", '\0', POPT_ARG_NONE, &gaussian_fit, 0,
"Use gaussian weights for flat histogram", "BOOLEAN"},
{"walkers", '\0', POPT_ARG_NONE, &walker_weights, 0,
"Use a walker optimization weight histogram method", "BOOLEAN"},
{"wang_landau", '\0', POPT_ARG_NONE, &wang_landau, 0,
"Use Wang-Landau histogram method", "BOOLEAN"},
{"wl_factor", '\0', POPT_ARG_DOUBLE | POPT_ARGFLAG_SHOW_DEFAULT, &wl_factor,
0, "Initial value of Wang-Landau factor", "DOUBLE"},
{"wl_fmod", '\0', POPT_ARG_DOUBLE | POPT_ARGFLAG_SHOW_DEFAULT, &wl_fmod, 0,
"Wang-Landau factor modifiction parameter", "DOUBLE"},
{"wl_threshold", '\0', POPT_ARG_DOUBLE | POPT_ARGFLAG_SHOW_DEFAULT,
&wl_threshold, 0, "Threhold for normalized standard deviation in "
"energy histogram at which to adjust Wang-Landau factor", "DOUBLE"},
{"wl_cutoff", '\0', POPT_ARG_DOUBLE | POPT_ARGFLAG_SHOW_DEFAULT,
&wl_cutoff, 0, "Cutoff for Wang-Landau factor", "DOUBLE"},
{"time", '\0', POPT_ARG_INT, &totime, 0,
"Timing of display information (seconds)", "INT"},
{"R", '\0', POPT_ARG_DOUBLE | POPT_ARGFLAG_SHOW_DEFAULT,
&R, 0, "Ball radius (for testing purposes; should always be 1)", "DOUBLE"},
{"test_weights", '\0', POPT_ARG_NONE, &test_weights, 0,
"Periodically print weight histogram during initialization", "BOOLEAN"},
{"debug", '\0', POPT_ARG_NONE, &debug, 0, "Debug mode", "BOOLEAN"},
POPT_AUTOHELP
POPT_TABLEEND
};
optCon = poptGetContext(NULL, argc, argv, optionsTable, 0);
poptSetOtherOptionHelp(optCon, "[OPTION...]\nNumber of balls and filling "
"fraction or cell dimensions are required arguments.");
int c = 0;
// go through arguments, set them based on optionsTable
while((c = poptGetNextOpt(optCon)) >= 0);
if (c < -1) {
fprintf(stderr, "\n%s: %s\n", poptBadOption(optCon, 0), poptStrerror(c));
return 1;
}
poptFreeContext(optCon);
// ----------------------------------------------------------------------------
// Verify we have reasonable arguments and set secondary parameters
// ----------------------------------------------------------------------------
// check that only one method is used
if(bool(no_weights) + bool(flat_histogram) + bool(gaussian_fit)
+ bool(wang_landau) + bool(walker_weights) + (fix_kT != 0) != 1){
printf("Exactly one histigram method must be selected!");
return 254;
}
if(sw.walls >= 2){
printf("Code cannot currently handle walls in more than one dimension.\n");
return 254;
}
if(sw.walls > 3){
printf("You cannot have walls in more than three dimensions.\n");
return 254;
}
if(well_width < 1){
printf("Interaction scale should be greater than (or equal to) 1.\n");
return 254;
}
// Adjust cell dimensions for desired filling fraction
const double fac = R*pow(4.0/3.0*M_PI*sw.N/(ff*sw.len[x]*sw.len[y]*sw.len[z]), 1.0/3.0);
for(int i = 0; i < 3; i++) sw.len[i] *= fac;
printf("\nSetting cell dimensions to (%g, %g, %g).\n",
sw.len[x], sw.len[y], sw.len[z]);
if (sw.N <= 0 || initialization_iterations < 0 || iterations < 0 || R <= 0 ||
neighbor_scale <= 0 || sw.dr <= 0 || translation_scale < 0 ||
sw.len[x] < 0 || sw.len[y] < 0 || sw.len[z] < 0) {
fprintf(stderr, "\nAll parameters must be positive.\n");
return 1;
}
sw.dr *= R;
const double eta = (double)sw.N*4.0/3.0*M_PI*R*R*R/(sw.len[x]*sw.len[y]*sw.len[z]);
if (eta > 1) {
fprintf(stderr, "\nYou're trying to cram too many balls into the cell. "
"They will never fit. Filling fraction: %g\n", eta);
return 7;
}
// If a filename was not selected, make a default
if (strcmp(filename, "default_filename") == 0) {
char *name_suffix = new char[10];
char *wall_tag = new char[10];
if(sw.walls == 0) sprintf(wall_tag,"periodic");
else if(sw.walls == 1) sprintf(wall_tag,"wall");
else if(sw.walls == 2) sprintf(wall_tag,"tube");
else if(sw.walls == 3) sprintf(wall_tag,"box");
if (fix_kT) {
sprintf(name_suffix, "-kT%g", fix_kT);
} else if (no_weights) {
sprintf(name_suffix, "-nw");
} else if (flat_histogram) {
sprintf(name_suffix, "-flat");
} else if (gaussian_fit) {
sprintf(name_suffix, "-gaussian");
} else if (wang_landau) {
sprintf(name_suffix, "-wang_landau");
} else if (walker_weights) {
sprintf(name_suffix, "-walkers");
} else {
name_suffix[0] = 0; // set name_suffix to the empty string
}
sprintf(filename, "%s-ww%04.2f-ff%04.2f-N%i%s",
wall_tag, well_width, eta, sw.N, name_suffix);
printf("\nUsing default file name: ");
delete[] name_suffix;
delete[] wall_tag;
}
else
printf("\nUsing given file name: ");
printf("%s\n",filename);
printf("------------------------------------------------------------------\n");
printf("Running %s with parameters:\n", argv[0]);
for(int i = 1; i < argc; i++) {
if(argv[i][0] == '-') printf("\n");
printf("%s ", argv[i]);
}
printf("\n");
if (totime > 0) printf("Timing information will be displayed.\n");
if (debug) printf("DEBUG MODE IS ENABLED!\n");
else printf("Debug mode disabled\n");
printf("------------------------------------------------------------------\n\n");
// ----------------------------------------------------------------------------
// Define sw_simulation variables
// ----------------------------------------------------------------------------
sw.iteration = 0; // start at zeroeth iteration
sw.state_of_max_interactions = 0;
sw.state_of_max_entropy = 0;
// translation distance should scale with ball radius
sw.translation_distance = translation_scale*R;
// neighbor radius should scale with radius and interaction scale
sw.neighbor_R = neighbor_scale*R*well_width;
// Find the upper limit to the maximum number of neighbors a ball could have
sw.max_neighbors = max_balls_within(2+neighbor_scale*well_width);
// Energy histogram
sw.interaction_distance = 2*R*well_width;
sw.energy_levels = sw.N/2*max_balls_within(sw.interaction_distance);
sw.energy_histogram = new long[sw.energy_levels]();
// Walkers
sw.current_walker_plus = false;
sw.walker_plus_threshold = 0;
sw.walker_minus_threshold = 0;
sw.walkers_plus = new long[sw.energy_levels]();
sw.walkers_total = new long[sw.energy_levels]();
// Energy weights, state density
int weight_updates = 0;
sw.ln_energy_weights = new double[sw.energy_levels]();
// Radial distribution function (RDF) histogram
long *g_energy_histogram = new long[sw.energy_levels]();
const int g_bins = round(min(min(min(sw.len[y],sw.len[z]),sw.len[x]),max_rdf_radius)
/ de_g / 2);
long **g_histogram = new long*[sw.energy_levels];
for(int i = 0; i < sw.energy_levels; i++)
g_histogram[i] = new long[g_bins]();
// Density histogram
const int density_bins = round(sw.len[wall_dim]/de_density);
const double bin_volume = sw.len[x]*sw.len[y]*sw.len[z]/sw.len[wall_dim]*de_density;
long **density_histogram = new long*[sw.energy_levels];
for(int i = 0; i < sw.energy_levels; i++)
density_histogram[i] = new long[density_bins]();
printf("memory use estimate = %.2g G\n\n",
8*double((6 + g_bins + density_bins)*sw.energy_levels)/1024/1024/1024);
sw.balls = new ball[sw.N];
if(totime < 0) totime = 10*sw.N;
// a guess for the number of iterations to run for initializing the histogram
int first_weight_update = sw.energy_levels;
// Initialize the random number generator with our seed
random::seed(seed);
// ----------------------------------------------------------------------------
// Set up the initial grid of balls
// ----------------------------------------------------------------------------
for(int i = 0; i < sw.N; i++) // initialize ball radii
sw.balls[i].R = R;
// Balls will be initially placed on a face centered cubic (fcc) grid
// Note that the unit cells need not be actually "cubic", but the fcc grid will
// be stretched to cell dimensions
const int spots_per_cell = 4; // spots in each fcc periodic unit cell
const int cells_floor = ceil(sw.N/spots_per_cell); // minimum number of cells
int cells[3]; // array to contain number of cells in x, y, and z dimensions
for(int i = 0; i < 3; i++){
cells[i] = ceil(pow(cells_floor*sw.len[i]*sw.len[i]
/(sw.len[(i+1)%3]*sw.len[(i+2)%3]),1.0/3.0));
}
// It is usefull to know our cell dimensions
double cell_width[3];
for(int i = 0; i < 3; i++) cell_width[i] = sw.len[i]/cells[i];
// Increase number of cells until all balls can be accomodated
int total_spots = spots_per_cell*cells[x]*cells[y]*cells[z];
int i = 0;
while(total_spots < sw.N) {
if(cell_width[i%3] <= cell_width[(i+1)%3] &&
cell_width[(i+1)%3] <= cell_width[(i+2)%3]) {
cells[i%3] += 1;
cell_width[i%3] = sw.len[i%3]/cells[i%3];
total_spots += spots_per_cell*cells[(i+1)%3]*cells[(i+2)%3];
}
i++;
}
// Define ball positions relative to cell position
vector3d* offset = new vector3d[4]();
offset[x] = vector3d(0,cell_width[y],cell_width[z])/2;
offset[y] = vector3d(cell_width[x],0,cell_width[z])/2;
offset[z] = vector3d(cell_width[x],cell_width[y],0)/2;
// Reserve some spots at random to be vacant
bool *spot_reserved = new bool[total_spots]();
int p; // Index of reserved spot
for(int i = 0; i < total_spots-sw.N; i++) {
p = floor(random::ran()*total_spots); // Pick a random spot index
if(spot_reserved[p] == false) // If it's not already reserved, reserve it
spot_reserved[p] = true;
else // Otherwise redo this index (look for a new spot)
i--;
}
// Place all balls in remaining spots
int b = 0;
vector3d cell_pos;
for(int i = 0; i < cells[x]; i++) {
for(int j = 0; j < cells[y]; j++) {
for(int k = 0; k < cells[z]; k++) {
for(int l = 0; l < 4; l++) {
if(!spot_reserved[i*(4*cells[z]*cells[y])+j*(4*cells[z])+k*4+l]) {
sw.balls[b].pos = vector3d(i*cell_width[x],j*cell_width[y],
k*cell_width[z]) + offset[l];
b++;
}
}
}
}
}
delete[] offset;
delete[] spot_reserved;
took("Placement");
// ----------------------------------------------------------------------------
// Print info about the initial configuration for troubleshooting
// ----------------------------------------------------------------------------
{
int most_neighbors =
initialize_neighbor_tables(sw.balls, sw.N, sw.neighbor_R + 2*sw.dr, sw.max_neighbors, sw.len,
sw.walls);
if (most_neighbors < 0) {
fprintf(stderr, "The guess of %i max neighbors was too low. Exiting.\n",
sw.max_neighbors);
return 1;
}
printf("Neighbor tables initialized.\n");
printf("The most neighbors is %i, whereas the max allowed is %i.\n",
most_neighbors, sw.max_neighbors);
}
// ----------------------------------------------------------------------------
// Make sure initial placement is valid
// ----------------------------------------------------------------------------
bool error = false, error_cell = false;
for(int i = 0; i < sw.N; i++) {
if (!in_cell(sw.balls[i], sw.len, sw.walls, sw.dr)) {
error_cell = true;
error = true;
}
for(int j = 0; j < i; j++) {
if (overlap(sw.balls[i], sw.balls[j], sw.len, sw.walls)) {
error = true;
break;
}
}
if (error) break;
}
if (error){
print_bad(sw.balls, sw.N, sw.len, sw.walls);
printf("Error in initial placement: ");
if(error_cell) printf("balls placed outside of cell.\n");
else printf("balls are overlapping.\n");
return 253;
}
fflush(stdout);
// ----------------------------------------------------------------------------
// Initialization of cell
// ----------------------------------------------------------------------------
double avg_neighbors = 0;
sw.interactions =
count_all_interactions(sw.balls, sw.N, sw.interaction_distance, sw.len, sw.walls);
// First, let us figure out what the max entropy point is.
sw.initialize_max_entropy_and_translation_distance();
if (gaussian_fit) {
sw.initialize_gaussian(10);
} else if (flat_histogram) {
{
sw.initialize_gaussian(log(1e40));
const int state_of_max_entropy = sw.state_of_max_entropy;
sw.initialize_max_entropy_and_translation_distance();
sw.state_of_max_entropy = state_of_max_entropy;
}
const double scale = log(10);
double width;
double range;
do {
width = sw.initialize_gaussian(scale);
range = sw.state_of_max_interactions - sw.state_of_max_entropy;
// Now shift to the max entropy state...
const int state_of_max_entropy = sw.state_of_max_entropy;
sw.initialize_max_entropy_and_translation_distance();
sw.state_of_max_entropy = state_of_max_entropy;
printf("***\n");
printf("*** Gaussian has width %.1f compared to range %.0f (ratio %.2f)\n",
width, range, width/range);
printf("***\n");
} while (width < 0.25*range);
} else if (fix_kT) {
sw.initialize_canonical(fix_kT);
} else if (wang_landau) {
sw.initialize_wang_landau(wl_factor, wl_threshold, wl_cutoff);
} else {
for(long iteration = 1;
iteration <= initialization_iterations + first_weight_update; iteration++) {
// ---------------------------------------------------------------
// Move each ball once
// ---------------------------------------------------------------
for(int i = 0; i < sw.N; i++) {
move_one_ball(i, sw.balls, sw.N, sw.len, sw.walls, sw.neighbor_R, sw.translation_distance,
sw.interaction_distance, sw.max_neighbors, sw.dr, &sw.moves,
sw.interactions, sw.ln_energy_weights);
sw.interactions += sw.moves.new_count - sw.moves.old_count;
sw.energy_histogram[sw.interactions]++;
if(walker_weights){
sw.walkers_total[sw.interactions]++;
if(sw.interactions >= sw.walker_minus_threshold)
sw.current_walker_plus = false;
else if(sw.interactions <= sw.walker_plus_threshold)
sw.current_walker_plus = true;
if(sw.current_walker_plus)
sw.walkers_plus[sw.interactions]++;
}
}
assert(sw.interactions ==
count_all_interactions(sw.balls, sw.N, sw.interaction_distance, sw.len, sw.walls));
// ---------------------------------------------------------------
// Update weights
// ---------------------------------------------------------------
if(!(no_weights || gaussian_fit)){
if(iteration == first_weight_update){
flat_hist(sw.energy_histogram, sw.ln_energy_weights, sw.energy_levels);
weight_updates++;
} else if((flat_histogram || walker_weights)
&& (iteration > first_weight_update)
&& ((iteration-first_weight_update)
% int(first_weight_update*uipow(2,weight_updates)) == 0)){
printf("Weight update: %d.\n", int(uipow(2,weight_updates)));
if (flat_histogram)
flat_hist(sw.energy_histogram, sw.ln_energy_weights, sw.energy_levels);
else if(walker_weights){
walker_hist(sw.energy_histogram, sw.ln_energy_weights, sw.energy_levels,
sw.walkers_plus, sw.walkers_total, &sw.moves);
}
weight_updates++;
if(test_weights) print_weights = true;
}
// for testing purposes; prints energy histogram and weight array
if(print_weights){
char *headerinfo = new char[4096];
sprintf(headerinfo,
"# cell dimensions: (%5.2f, %5.2f, %5.2f), walls: %i,"
" de_density: %g, de_g: %g\n# seed: %li, N: %i, R: %f,"
" well_width: %g, translation_distance: %g\n"
"# initialization_iterations: %li, neighbor_scale: %g, dr: %g,"
" energy_levels: %i\n",
sw.len[0], sw.len[1], sw.len[2], sw.walls, de_density, de_g, seed, sw.N, R,
well_width, sw.translation_distance, initialization_iterations,
neighbor_scale, sw.dr, sw.energy_levels);
char *countinfo = new char[4096];
sprintf(countinfo,
"# iteration: %li, working moves: %li, total moves: %li, "
"acceptance rate: %g\n",
iteration, sw.moves.working, sw.moves.total,
double(sw.moves.working)/sw.moves.total);
const char *testdir = "test";
char *w_fname = new char[1024];
char *e_fname = new char[1024];
mkdir(dir, 0777); // create save directory
sprintf(w_fname, "%s/%s", dir, testdir);
mkdir(w_fname, 0777); // create test directory
sprintf(w_fname, "%s/%s/%s-w%02i.dat",
dir, testdir, filename, weight_updates);
sprintf(e_fname, "%s/%s/%s-E%02i.dat",
dir, testdir, filename, weight_updates);
FILE *w_out = fopen(w_fname, "w");
if (!w_out) {
fprintf(stderr, "Unable to create %s!\n", w_fname);
exit(1);
}
fprintf(w_out, "%s", headerinfo);
fprintf(w_out, "%s", countinfo);
fprintf(w_out, "\n# interactions value\n");
for(int i = 0; i < sw.energy_levels; i++)
fprintf(w_out, "%i %f\n", i, sw.ln_energy_weights[i]);
fclose(w_out);
FILE *e_out = fopen((const char *)e_fname, "w");
fprintf(e_out, "%s", headerinfo);
fprintf(e_out, "%s", countinfo);
fprintf(e_out, "\n# interactions counts\n");
for(int i = 0; i < sw.energy_levels; i++)
fprintf(e_out, "%i %ld\n",i,sw.energy_histogram[i]);
fclose(e_out);
delete[] headerinfo;
delete[] countinfo;
delete[] w_fname;
delete[] e_fname;
print_weights = false;
}
}
// ---------------------------------------------------------------
// Print out timing information if desired
// ---------------------------------------------------------------
if (totime > 0 && iteration % totime == 0) {
char *iter = new char[1024];
sprintf(iter, "%i iterations", totime);
took(iter);
delete[] iter;
printf("Iteration %li, acceptance rate of %g, translation_distance: %g.\n",
iteration, (double)sw.moves.working/sw.moves.total,
sw.translation_distance);
printf("We've had %g updates per kilomove and %g informs per kilomoves, "
"for %g informs per update.\n",
1000.0*sw.moves.updates/sw.moves.total,
1000.0*sw.moves.informs/sw.moves.total,
(double)sw.moves.informs/sw.moves.updates);
const long checks_without_tables = sw.moves.total*sw.N;
int total_neighbors = 0;
int most_neighbors = 0;
for(int i = 0; i < sw.N; i++) {
total_neighbors += sw.balls[i].num_neighbors;
most_neighbors = max(sw.balls[i].num_neighbors, most_neighbors);
}
avg_neighbors = double(total_neighbors)/sw.N;
const long checks_with_tables = sw.moves.total*avg_neighbors
+ sw.N*sw.moves.updates;
printf("We've done about %.3g%% of the distance calculations we would "
"have done without tables.\n",
100.0*checks_with_tables/checks_without_tables);
printf("The max number of neighbors is %i, whereas the most we have is "
"%i.\n", sw.max_neighbors, most_neighbors);
printf("Neighbor scale is %g and avg. number of neighbors is %g.\n\n",
neighbor_scale, avg_neighbors);
fflush(stdout);
}
}
}
{
// Now let's iterate to the point where we are at maximum
// probability before we do teh real simulation.
const double st = sw.state_of_max_entropy;
sw.initialize_max_entropy_and_translation_distance();
sw.state_of_max_entropy = st;
}
took("Initialization");
// ----------------------------------------------------------------------------
// Generate info to put in save files
// ----------------------------------------------------------------------------
mkdir(dir, 0777); // create save directory
char *headerinfo = new char[4096];
sprintf(headerinfo,
"# cell dimensions: (%5.2f, %5.2f, %5.2f), walls: %i,"
" de_density: %g, de_g: %g\n# seed: %li, N: %i, R: %f,"
" well_width: %g, translation_distance: %g\n"
"# initialization_iterations: %li, neighbor_scale: %g, dr: %g,"
" energy_levels: %i\n",
sw.len[0], sw.len[1], sw.len[2], sw.walls, de_density, de_g, seed, sw.N, R,
well_width, sw.translation_distance, initialization_iterations,
neighbor_scale, sw.dr, sw.energy_levels);
char *e_fname = new char[1024];
sprintf(e_fname, "%s/%s-E.dat", dir, filename);
char *w_fname = new char[1024];
sprintf(w_fname, "%s/%s-lnw.dat", dir, filename);
char *density_fname = new char[1024];
sprintf(density_fname, "%s/%s-density-%i.dat", dir, filename, sw.N);
char *g_fname = new char[1024];
sprintf(g_fname, "%s/%s-g.dat", dir, filename);
// ----------------------------------------------------------------------------
// MAIN PROGRAM LOOP
// ----------------------------------------------------------------------------
clock_t output_period = CLOCKS_PER_SEC; // start at outputting every minute
// top out at one hour interval
clock_t max_output_period = clock_t(CLOCKS_PER_SEC)*60*30;
clock_t last_output = clock(); // when we last output data
sw.moves.total = 0;
sw.moves.working = 0;
// Reset energy histogram
for(int i = 0; i < sw.energy_levels; i++)
sw.energy_histogram[i] = 0;
for(long iteration = 1; iteration <= iterations; iteration++) {
// ---------------------------------------------------------------
// Move each ball once, add to energy histogram
// ---------------------------------------------------------------
for(int i = 0; i < sw.N; i++) {
move_one_ball(i, sw.balls, sw.N, sw.len, sw.walls, sw.neighbor_R, sw.translation_distance,
sw.interaction_distance, sw.max_neighbors, sw.dr, &sw.moves,
sw.interactions, sw.ln_energy_weights);
sw.interactions += sw.moves.new_count - sw.moves.old_count;
sw.energy_histogram[sw.interactions]++;
}
assert(sw.interactions ==
count_all_interactions(sw.balls, sw.N, sw.interaction_distance, sw.len, sw.walls));
// ---------------------------------------------------------------
// Add data to density and RDF histograms
// ---------------------------------------------------------------
// Density histogram
if(sw.walls){
for(int i = 0; i < sw.N; i++){
density_histogram[sw.interactions]
[int(floor(sw.balls[i].pos[wall_dim]/de_density))] ++;
}
}
// RDF
if(!sw.walls){
g_energy_histogram[sw.interactions]++;
for(int i = 0; i < sw.N; i++){
for(int j = 0; j < sw.N; j++){
if(i != j){
const vector3d r = periodic_diff(sw.balls[i].pos, sw.balls[j].pos, sw.len,
sw.walls);
const int r_i = floor(r.norm()/de_g);
if(r_i < g_bins) g_histogram[sw.interactions][r_i]++;
}
}
}
}
// ---------------------------------------------------------------
// Save to file
// ---------------------------------------------------------------
const clock_t now = clock();
if ((now - last_output > output_period) || iteration == iterations) {
last_output = now;
assert(last_output);
if (output_period < max_output_period/2) output_period *= 2;
else if (output_period < max_output_period)
output_period = max_output_period;
const double secs_done = double(now)/CLOCKS_PER_SEC;
const int seconds = int(secs_done) % 60;
const int minutes = int(secs_done / 60) % 60;
const int hours = int(secs_done / 3600) % 24;
const int days = int(secs_done / 86400);
printf("Saving data after %i days, %02i:%02i:%02i, %li iterations "
"complete.\n", days, hours, minutes, seconds, iteration);
fflush(stdout);
char *countinfo = new char[4096];
sprintf(countinfo,
"# iteration: %li, working moves: %li, total moves: %li, "
"acceptance rate: %g\n",
iteration, sw.moves.working, sw.moves.total,
double(sw.moves.working)/sw.moves.total);
// Save energy histogram
FILE *e_out = fopen((const char *)e_fname, "w");
fprintf(e_out, "%s", headerinfo);
fprintf(e_out, "%s", countinfo);
fprintf(e_out, "\n# interactions counts\n");
for(int i = 0; i < sw.energy_levels; i++)
if(sw.energy_histogram[i] != 0)
fprintf(e_out, "%i %ld\n",i,sw.energy_histogram[i]);
fclose(e_out);
// Save weights histogram
FILE *w_out = fopen((const char *)w_fname, "w");
fprintf(w_out, "%s", headerinfo);
fprintf(w_out, "%s", countinfo);
fprintf(w_out, "\n# interactions ln(weight)\n");
for(int i = 0; i < sw.energy_levels; i++)
if(sw.energy_histogram[i] != 0){
fprintf(w_out, "%i %g\n",i,sw.ln_energy_weights[i]);
}
fclose(w_out);
// Save RDF
if(!sw.walls){
FILE *g_out = fopen((const char *)g_fname, "w");
fprintf(g_out, "%s", headerinfo);
fprintf(g_out, "%s", countinfo);
fprintf(g_out, "\n# data table containing values of g");
fprintf(g_out, "\n# first column reserved for specifying energy level");
fprintf(g_out, "\n# column number rn (starting from the second column, "
"counting from zero) corresponds to radius r given by "
"r = (rn + 0.5) * de_g");
const double density = sw.N/sw.len[x]/sw.len[y]/sw.len[z];
const double total_vol = sw.len[x]*sw.len[y]*sw.len[z];
for(int i = 0; i < sw.energy_levels; i++){
if(g_histogram[i][g_bins-1] > 0){ // if we have RDF data at this energy
fprintf(g_out, "\n%i",i);
for(int r_i = 0; r_i < g_bins; r_i++) {
const double probability = (double)g_histogram[i][r_i]
/ g_energy_histogram[i];
const double r = (r_i + 0.5) * de_g;
const double shell_vol =
4.0/3.0*M_PI*(uipow(r+de_g/2, 3) - uipow(r-de_g/2, 3));
const double n2 = probability/total_vol/shell_vol;
const double g = n2/sqr(density);
fprintf(g_out, " %8.5f", g);
}
}
}
fclose(g_out);
}
// Saving density data
if(sw.walls){
FILE *densityout = fopen((const char *)density_fname, "w");
fprintf(densityout, "%s", headerinfo);
fprintf(densityout, "%s", countinfo);
fprintf(densityout, "\n# data table containing densities in slabs "
"(bins) of thickness de_density away from a wall");
fprintf(densityout, "\n# row number corresponds to energy level");
fprintf(densityout, "\n# column number dn (counting from zero) "
"corresponds to distance d from wall given by "
"d = (dn + 0.5) * de_density");
for(int i = 0; i < sw.energy_levels; i++){
fprintf(densityout, "\n");
for(int r_i = 0; r_i < density_bins; r_i++) {
const double bin_density =
(double)density_histogram[i][r_i]
*sw.N/sw.energy_histogram[i]/bin_volume;
fprintf(densityout, "%8.5f ", bin_density);
}
}
fclose(densityout);
}
delete[] countinfo;
}
}
// ----------------------------------------------------------------------------
// END OF MAIN PROGRAM LOOP
// ----------------------------------------------------------------------------
delete[] sw.balls;
delete[] sw.ln_energy_weights;
delete[] sw.energy_histogram;
delete[] g_histogram;
delete[] density_histogram;
delete[] headerinfo;
return 0;
}
int main(int argc, const char *argv[]) {
printf("Running %s version %s\n", argv[0], version_identifier());
for (int i=0; argv[i]; i++) {
printf("%s ", argv[i]);
}
printf("\n");
took("Starting program");
// ----------------------------------------------------------------------------
// Define "Constants" -- set from arguments then unchanged
// ----------------------------------------------------------------------------
// NOTE: debug can slow things down VERY much
int debug = false;
sw_simulation sw;
sw.sticky_wall = 0;
sw.len[0] = sw.len[1] = sw.len[2] = 1;
sw.walls = 0;
sw.N = 10;
sw.translation_scale = 0.05;
unsigned long int seed = 0;
char *data_dir = new char[1024];
sprintf(data_dir, "free-energy-data");
char *filename = new char[1024];
sprintf(filename, "default_filename");
char *filename_suffix = new char[1024];
sprintf(filename_suffix, "default_filename_suffix");
long simulation_runs = 1000000;
double acceptance_goal = .4;
double R = 1;
const double well_width = 1;
double ff = 0.3;
double ff_small = -1;
bool force_cube=false;
bool pack_and_save_cube=false;
double neighbor_scale = 2;
double de_g = 0.05;
double max_rdf_radius = 10;
int totime = 0;
double scaling_factor = 1.0;
int small_cell_check_period = (1 * sw.N * sw.N)/10;
poptContext optCon;
// ----------------------------------------------------------------------------
// Set values from parameters
// ----------------------------------------------------------------------------
poptOption optionsTable[] = {
{"N", '\0', POPT_ARG_INT, &sw.N, 0, "Number of balls to simulate", "INT"},
{"ff", '\0', POPT_ARG_DOUBLE, &ff, 0, "Filling fraction. If specified, the "
"cell dimensions are adjusted accordingly without changing the shape of "
"the cell."},
{"ff_small", '\0', POPT_ARG_DOUBLE, &ff_small, 0, "Small filling fraction. If specified, "
"This sets the desired filling fraction of the shrunk cell. Otherwise it defaults to ff."},
{"force_cube", '\0', POPT_ARG_NONE, &force_cube, 0, "forces box to be a cube", "BOOLEAN"},
{"pack_and_save_cube", '\0', POPT_ARG_NONE, &pack_and_save_cube, 0, "packs cube, save positions, then returns", "BOOLEAN"},
{"walls", '\0', POPT_ARG_INT | POPT_ARGFLAG_SHOW_DEFAULT, &sw.walls, 0,
"Number of walled dimensions (dimension order: x,y,z)", "INT"},
{"runs", '\0', POPT_ARG_LONG | POPT_ARGFLAG_SHOW_DEFAULT, &simulation_runs,
0, "Number of \"runs\" for which to run the simulation", "INT"},
{"de_g", '\0', POPT_ARG_DOUBLE | POPT_ARGFLAG_SHOW_DEFAULT, &de_g, 0,
"Resolution of distribution functions", "DOUBLE"},
{"max_rdf_radius", '\0', POPT_ARG_DOUBLE | POPT_ARGFLAG_SHOW_DEFAULT,
&max_rdf_radius, 0, "Set maximum radius for RDF data collection", "DOUBLE"},
{"lenx", '\0', POPT_ARG_DOUBLE, &sw.len[x], 0,
"Relative cell size in x dimension", "DOUBLE"},
{"leny", '\0', POPT_ARG_DOUBLE, &sw.len[y], 0,
"Relative cell size in y dimension", "DOUBLE"},
{"lenz", '\0', POPT_ARG_DOUBLE, &sw.len[z], 0,
"Relative cell size in z dimension", "DOUBLE"},
{"filename", '\0', POPT_ARG_STRING | POPT_ARGFLAG_SHOW_DEFAULT, &filename, 0,
"Base of output file names", "STRING"},
{"filename_suffix", '\0', POPT_ARG_STRING | POPT_ARGFLAG_SHOW_DEFAULT,
&filename_suffix, 0, "Output file name suffix", "STRING"},
{"data_dir", '\0', POPT_ARG_STRING | POPT_ARGFLAG_SHOW_DEFAULT, &data_dir, 0,
"Directory in which to save data", "data_dir"},
{"neighbor_scale", '\0', POPT_ARG_DOUBLE | POPT_ARGFLAG_SHOW_DEFAULT,
&neighbor_scale, 0, "Ratio of neighbor sphere radius to interaction scale "
"times ball radius. Drastically reduces collision detections","DOUBLE"},
{"translation_scale", '\0', POPT_ARG_DOUBLE | POPT_ARGFLAG_SHOW_DEFAULT,
&sw.translation_scale, 0, "Standard deviation for translations of balls, "
"relative to ball radius", "DOUBLE"},
{"seed", '\0', POPT_ARG_INT | POPT_ARGFLAG_SHOW_DEFAULT, &seed, 0,
"Seed for the random number generator", "INT"},
{"acceptance_goal", '\0', POPT_ARG_DOUBLE | POPT_ARGFLAG_SHOW_DEFAULT,
&acceptance_goal, 0, "Goal to set the acceptance rate", "DOUBLE"},
{"time", '\0', POPT_ARG_INT, &totime, 0,
"Timing of display information (seconds)", "INT"},
{"R", '\0', POPT_ARG_DOUBLE | POPT_ARGFLAG_SHOW_DEFAULT,
&R, 0, "Ball radius (for testing purposes; should always be 1)", "DOUBLE"},
{"debug", '\0', POPT_ARG_NONE, &debug, 0, "Debug mode", "BOOLEAN"},
{"sf", '\0', POPT_ARG_DOUBLE, &scaling_factor, 0,
"Factor by which to scale the small cell", "DOUBLE"},
{"sc_period", '\0', POPT_ARG_INT, &small_cell_check_period, 0,
"Check the small cell every P iterations", "INT"},
POPT_AUTOHELP
POPT_TABLEEND
};
optCon = poptGetContext(NULL, argc, argv, optionsTable, 0);
poptSetOtherOptionHelp(optCon, "[OPTION...]\nNumber of balls and filling "
"fraction or cell dimensions are required arguments.");
int c = 0;
// go through arguments, set them based on optionsTable
while((c = poptGetNextOpt(optCon)) >= 0);
if (c < -1) {
fprintf(stderr, "\n%s: %s\n", poptBadOption(optCon, 0), poptStrerror(c));
return 1;
}
poptFreeContext(optCon);
// ----------------------------------------------------------------------------
// Verify we have reasonable arguments and set secondary parameters
// ----------------------------------------------------------------------------
if(sw.walls >= 2){
printf("Code cannot currently handle walls in more than one dimension.\n");
return 254;
}
if(sw.walls > 3){
printf("You cannot have walls in more than three dimensions.\n");
return 254;
}
if(well_width < 1){
printf("Interaction scale should be greater than (or equal to) 1.\n");
return 254;
}
if(ff_small != -1 && scaling_factor != 1.0){
printf("You can't specify both the small filling fraction and the scaling factor.");
return 1;
}
if (ff != 0) {
// The user specified a filling fraction, so we must make it so!
const double volume = 4*M_PI/3*R*R*R*sw.N/ff;
const double min_cell_width = 2*sqrt(2)*R; // minimum cell width
const int numcells = (sw.N+3)/4; // number of unit cells we need
const int max_cubic_width
= pow(volume/min_cell_width/min_cell_width/min_cell_width, 1.0/3);
if (max_cubic_width*max_cubic_width*max_cubic_width >= numcells) {
// We can get away with a cubic cell, so let's do so. Cubic
// cells are nice and comfortable!
sw.len[x] = sw.len[y] = sw.len[z] = pow(volume, 1.0/3);
} else {
printf("N = %d\n", sw.N);
printf("ff = %g\n", ff);
printf("min_cell_width = %g\n", min_cell_width);
printf("volume**1/3 = %g\n", pow(volume, 1.0/3));
printf("max_cubic_width**3 = %d, numcells = %d\n",
max_cubic_width*max_cubic_width*max_cubic_width, numcells);
// A cubic cell won't work with our initialization routine, so
// let's go with a lopsided cell that should give us something
// that will work.
int xcells = int( pow(numcells, 1.0/3) );
int cellsleft = (numcells + xcells - 1)/xcells;
int ycells = int( sqrt(cellsleft) );
int zcells = (cellsleft + ycells - 1)/ycells;
// The above should give a zcells that is largest, followed by
// ycells and then xcells. Thus we make the lenz just small
// enough to fit these cells, and so on, to make the cell as
// close to cubic as possible.
sw.len[z] = zcells*min_cell_width;
if (xcells == ycells) {
sw.len[x] = sw.len[y] = sqrt(volume/sw.len[z]);
} else {
sw.len[y] = min_cell_width*ycells;
sw.len[x] = volume/sw.len[y]/sw.len[z];
}
printf("Using lopsided %d x %d x %d cell (total goal %d)\n",
xcells, ycells, zcells, numcells);
}
}
// if the user didn't specifiy a small filling fraction, then we should get it.
if(ff_small == -1){
ff_small = (4*M_PI/3*R*R*R*sw.N)/
(sw.len[x]*sw.len[y]*sw.len[z]*scaling_factor*scaling_factor*scaling_factor);
}
// if they did, then we need to get the scale factor
else{
scaling_factor = std::cbrt(ff/ff_small);
}
printf("\nSetting cell dimensions to (%g, %g, %g).\n",
sw.len[x], sw.len[y], sw.len[z]);
printf("\nFilling fraction of small cell is %g", ff_small);
if (sw.N <= 0 || simulation_runs < 0 || R <= 0 ||
neighbor_scale <= 0 || sw.translation_scale < 0 ||
sw.len[x] < 0 || sw.len[y] < 0 || sw.len[z] < 0) {
fprintf(stderr, "\nAll parameters must be positive.\n");
return 1;
}
const double eta = (double)sw.N*4.0/3.0*M_PI*R*R*R/(sw.len[x]*sw.len[y]*sw.len[z]);
if (eta > 1) {
fprintf(stderr, "\nYou're trying to cram too many balls into the cell. "
"They will never fit. Filling fraction: %g\n", eta);
return 7;
}
// If a filename was not selected, make a default
if (strcmp(filename, "default_filename") == 0) {
char *wall_tag = new char[100];
if(sw.walls == 0) sprintf(wall_tag,"periodic");
else if(sw.walls == 1) sprintf(wall_tag,"wall");
else if(sw.walls == 2) sprintf(wall_tag,"tube");
else if(sw.walls == 3) sprintf(wall_tag,"box");
sprintf(filename, "%s-ww%04.2f-ff%04.2f-N%i-sf%f",
wall_tag, well_width, eta, sw.N, scaling_factor);
printf("\nUsing default file name: ");
delete[] wall_tag;
}
else
printf("\nUsing given file name: ");
// If a filename suffix was specified, add it
if (strcmp(filename_suffix, "default_filename_suffix") != 0)
sprintf(filename, "%s-%s", filename, filename_suffix);
printf("%s\n",filename);
printf("------------------------------------------------------------------\n");
printf("Running %s with parameters:\n", argv[0]);
for(int i = 1; i < argc; i++) {
if(argv[i][0] == '-') printf("\n");
printf("%s ", argv[i]);
}
printf("\nUsing scaling factor of %f", scaling_factor);
printf("\n");
if (totime > 0) printf("Timing information will be displayed.\n");
if (debug) printf("DEBUG MODE IS ENABLED!\n");
else printf("Debug mode disabled\n");
printf("------------------------------------------------------------------\n\n");
// ----------------------------------------------------------------------------
// Define sw_simulation variables
// ----------------------------------------------------------------------------
sw.iteration = 0; // start at zeroeth iteration
sw.max_entropy_state = 0;
sw.min_energy_state = 0;
sw.energy = 0;
sw.min_important_energy = 0;
// translation distance should scale with ball radius
sw.translation_scale *= R;
// neighbor radius should scale with radius and interaction scale
sw.neighbor_R = neighbor_scale*R*well_width;
// Find the upper limit to the maximum number of neighbors a ball could have
sw.max_neighbors = max_balls_within(2+neighbor_scale*well_width);
// Energy histogram and weights
sw.interaction_distance = 2*R*well_width;
sw.energy_levels = 1; // hard spheres can only have one energy!
sw.energy_histogram = new long[sw.energy_levels]();
sw.ln_energy_weights = new double[sw.energy_levels]();
// Observed and sampled energies
sw.pessimistic_observation = new bool[sw.energy_levels]();
sw.pessimistic_samples = new long[sw.energy_levels]();
sw.optimistic_samples = new long[sw.energy_levels]();
// Transitions from one energy to another
sw.biggest_energy_transition = max_balls_within(sw.interaction_distance);
sw.transitions_table =
new long[sw.energy_levels*(2*sw.biggest_energy_transition+1)]();
// Walker histograms
sw.walkers_up = new long[sw.energy_levels]();
printf("memory use estimate = %.2g G\n\n",
8*double(6*sw.energy_levels)/1024/1024/1024);
sw.balls = new ball[sw.N];
if(totime < 0) totime = 10*sw.N;
// Initialize the random number generator with our seed
random::seed(seed);
// ----------------------------------------------------------------------------
// Set up the initial grid of balls
// ----------------------------------------------------------------------------
for(int i = 0; i < sw.N; i++) // initialize ball radii
sw.balls[i].R = R;
//########################### pack and save ####################
if(pack_and_save_cube==true){
INITBOX *box=load_cube(data_dir);
if(box!=NULL && box->numAtoms<sw.N) {delete box; box=NULL;}
if(box!=NULL){//---------loaded baseAtoms up to max of sw.N
printf("loading from baseAtoms.txt\n");
for(int count=0;count<(100*box->numAtoms);count++){
//mixes indices so the culled atoms are random
//atoms are only culled from the end...
int n1=floor(random::ran()*(box->numAtoms));
int n2=floor(random::ran()*(box->numAtoms));
double xTemp=box->list[n1].x;
double yTemp=box->list[n1].y;
double zTemp=box->list[n1].z;
box->list[n1].x=box->list[n2].x;
box->list[n1].y=box->list[n2].y;
box->list[n1].z=box->list[n2].z;
box->list[n2].x=xTemp;
box->list[n2].y=yTemp;
box->list[n2].z=zTemp;
}
//box2 is used to cull atoms from the end (if needed)
//box2 is simulated to mix the atoms up after culling
INITBOX *box2=new INITBOX(box->lx);
for(int i=0;i<sw.N;i++) box2->addAtom(box->list[i].x,box->list[i].y,box->list[i].z);
delete box;
box2->temperature=1000.0;
for(int i=0;i<100;i++) box2->simulate(sw.N*100);//mix box
sw.len[x] = sw.len[y] = sw.len[z] = box2->lx;
for(int i=0;i<sw.N;i++) {
sw.balls[i].pos=vector3d(box2->list[i].x,box2->list[i].y,box2->list[i].z);
}
delete box2;
}
else{//if no baseAtoms.txt then try to pack the box
if(ff==0){printf("must initialize using --ff\n"); return 254;}
printf("building baseAtoms.txt\n");
const double volume = 4*M_PI/3*R*R*R*sw.N/ff;
sw.len[x] = sw.len[y] = sw.len[z] = pow(volume, 1.0/3);
if(pack_cube(sw)==false) {printf("could not fill box\n"); return 254;}
}//done initializing positions
mkdir(data_dir, 0777); // create save directory
char *posData = new char[4096];
sprintf(posData,"%s/baseAtoms.txt",data_dir);
FILE *pos_out = fopen((const char *)posData, "w");
sprintf(posData,"L = %g\nN = %i\n",sw.len[x],sw.N);
fprintf(pos_out,"%s",posData);
for(int i=0;i<sw.N;i++){
sprintf(posData,"%g %g %g",
sw.balls[i].pos.x,sw.balls[i].pos.y,sw.balls[i].pos.z);
fprintf(pos_out,"%s",posData);
if(i+1<sw.N) fprintf(pos_out,"\n");
}
fclose(pos_out);
delete[] posData;
took("Placement");
return 0;
}
//########################### DONE pack and save #################
if(force_cube==true){//try to load baseAtoms.txt
if(ff==0){printf("must initialize using --ff\n"); return 254;}
printf("attempting to load baseAtoms.txt\n");
const double volume = 4*M_PI/3*R*R*R*sw.N/ff;
sw.len[x] = sw.len[y] = sw.len[z] = pow(volume, 1.0/3);
INITBOX *box=load_cube(data_dir);
if(box==NULL) {
printf("requires initialization on the smallest box\nuse the --pack_and_save --ff -N flags\n");
return 254; }
if(box->numAtoms<sw.N){
printf("boxAtoms.txt contains less atoms than expected\n");
delete box;
return 254; }
if(box->lx>sw.len[x]){
printf("baseAtoms must be in a box smaller than current simulation\n");
delete box;
return 254; }
box->temperature=1000.0;
for(int i=0;i<100;i++) box->simulate(sw.N*100);//mix box
double scaleFactor=sw.len[x]/box->lx;
for(int i=0;i<sw.N;i++){
double x=(box->list[i].x)*scaleFactor;
double y=(box->list[i].y)*scaleFactor;
double z=(box->list[i].z)*scaleFactor;
sw.balls[i].pos=vector3d(x,y,z);
}
delete box;
}
else {
// Balls will be initially placed on a face centered cubic (fcc) grid
// Note that the unit cells need not be actually "cubic", but the fcc grid will
// be stretched to cell dimensions
const double min_cell_width = 2*sqrt(2)*R; // minimum cell width
const int spots_per_cell = 4; // spots in each fcc periodic unit cell
int cells[3]; // array to contain number of cells in x, y, and z dimensions
for(int i = 0; i < 3; i++){
cells[i] = int(sw.len[i]/min_cell_width); // max number of cells that will fit
}
// It is usefull to know our cell dimensions
double cell_width[3];
for(int i = 0; i < 3; i++) cell_width[i] = sw.len[i]/cells[i];
// If we made our cells to small, return with error
for(int i = 0; i < 3; i++){
if(cell_width[i] < min_cell_width){
printf("Placement cell size too small: (%g, %g, %g) coming from (%g, %g, %g)\n",
cell_width[0],cell_width[1],cell_width[2],
sw.len[0], sw.len[1], sw.len[2]);
printf("Minimum allowed placement cell width: %g\n",min_cell_width);
printf("Total simulation cell dimensions: (%g, %g, %g)\n",
sw.len[0],sw.len[1],sw.len[2]);
printf("Fixing the chosen ball number, filling fractoin, and relative\n"
" simulation cell dimensions simultaneously does not appear to be possible\n");
return 176;
}
}
// Define ball positions relative to cell position
vector3d* offset = new vector3d[4]();
offset[x] = vector3d(0,cell_width[y],cell_width[z])/2;
offset[y] = vector3d(cell_width[x],0,cell_width[z])/2;
offset[z] = vector3d(cell_width[x],cell_width[y],0)/2;
// Reserve some spots at random to be vacant
const int total_spots = spots_per_cell*cells[x]*cells[y]*cells[z];
bool *spot_reserved = new bool[total_spots]();
int p; // Index of reserved spot
for(int i = 0; i < total_spots-sw.N; i++) {
p = floor(random::ran()*total_spots); // Pick a random spot index
if(spot_reserved[p] == false) // If it's not already reserved, reserve it
spot_reserved[p] = true;
else // Otherwise redo this index (look for a new spot)
i--;
}
// Place all balls in remaining spots
int b = 0;
for(int i = 0; i < cells[x]; i++) {
for(int j = 0; j < cells[y]; j++) {
for(int k = 0; k < cells[z]; k++) {
for(int l = 0; l < 4; l++) {
if(!spot_reserved[i*(4*cells[z]*cells[y])+j*(4*cells[z])+k*4+l]) {
sw.balls[b].pos = vector3d(i*cell_width[x],j*cell_width[y],
k*cell_width[z]) + offset[l];
b++;
}
}
}
}
}
delete[] offset;
delete[] spot_reserved;
}
took("Placement");
// ----------------------------------------------------------------------------
// Print info about the initial configuration for troubleshooting
// ----------------------------------------------------------------------------
{
int most_neighbors =
initialize_neighbor_tables(sw.balls, sw.N, sw.neighbor_R,
sw.max_neighbors, sw.len, sw.walls);
if (most_neighbors < 0) {
fprintf(stderr, "The guess of %i max neighbors was too low. Exiting.\n",
sw.max_neighbors);
return 1;
}
printf("Neighbor tables initialized.\n");
printf("The most neighbors is %i, whereas the max allowed is %i.\n",
most_neighbors, sw.max_neighbors);
}
// ----------------------------------------------------------------------------
// Make sure initial placement is valid
// ----------------------------------------------------------------------------
for(int i = 0; i < sw.N; i++) {
for(int j = 0; j < i; j++) {
if (overlap(sw.balls[i], sw.balls[j], sw.len, sw.walls)) {
print_bad(sw.balls, sw.N, sw.len, sw.walls);
printf("Error in initial placement: balls are overlapping.\n");
return 253;
}
}
}
fflush(stdout);
// ----------------------------------------------------------------------------
// Initialization of cell
// ----------------------------------------------------------------------------
sw.initialize_translation_distance();
// --------------------------------------------------------------------------
// end initilization routine.
// --------------------------------------------------------------------------
// ----------------------------------------------------------------------------
// Generate info to put in save files
// ----------------------------------------------------------------------------
mkdir(data_dir, 0777); // create save directory
char *headerinfo = new char[4096];
sprintf(headerinfo,
"# version: %s\n"
"# cell dimensions: (%g, %g, %g)\n"
"# walls: %i\n"
"# de_g: %g\n"
"# seed: %li\n"
"# N: %i\n"
"# R: %f\n"
"# well_width: %g\n"
"# translation_scale: %g\n"
"# neighbor_scale: %g\n"
"# scaling factor: %g\n"
"# ff: %g\n"
"# ff_small: %g\n",
version_identifier(),
sw.len[0], sw.len[1], sw.len[2], sw.walls, de_g, seed, sw.N, R,
well_width, sw.translation_scale, neighbor_scale, scaling_factor, ff, ff_small);
char *g_fname = new char[1024];
sprintf(g_fname, "%s/%s.dat", data_dir, filename);
took("Initialization");
// ----------------------------------------------------------------------------
// MAIN PROGRAM LOOP
// ----------------------------------------------------------------------------
sw.moves.total = 0;
sw.moves.working = 0;
sw.iteration = 0;
// tracking for free energy
int current_valid_run = 0;
int current_failed_run = 0;
int longest_valid_run = 0;
int longest_failed_run = 0;
int total_checks_of_small_cell = 0;
int total_valid_small_checks = 0;
int total_failed_small_checks = 0;
int valid_runs = 0;
int failed_runs = 0;
double average_valid_run = 0;
double average_failed_run = 0;
// Reset energy histogram and sample counts
for(int i = 0; i < sw.energy_levels; i++){
sw.energy_histogram[i] = 0;
sw.pessimistic_samples[i] = 0;
sw.optimistic_samples[i] = 0;
}
do {
// ---------------------------------------------------------------
// Move each ball once, add to energy histogram
// ---------------------------------------------------------------
for(int i = 0; i < sw.N; i++){
sw.move_a_ball();
}
// just hacking stuff in to see what works
// do the small bit every 100 n^2 iterations for now
if (sw.iteration % small_cell_check_period == 0) {
total_checks_of_small_cell++;
if(overlap_in_small_cell(sw, scaling_factor)){
total_failed_small_checks++;
if (current_failed_run == 0){
// then valid run just ended so record it
valid_runs++;
if(current_valid_run > longest_valid_run)
longest_valid_run = current_valid_run;
average_valid_run = average_valid_run + (current_valid_run - average_valid_run)/valid_runs;
current_valid_run = 0;
}
current_failed_run++;
if(debug){printf("%i - false\n", current_failed_run);}
}
else{
total_valid_small_checks++;
if (current_valid_run == 0){
// then failed run just ended so record it
failed_runs++;
if(current_failed_run > longest_failed_run)
longest_failed_run = current_failed_run;
average_failed_run = average_failed_run + (current_failed_run - average_failed_run)/failed_runs;
current_failed_run = 0;
}
current_valid_run++;
if(debug){printf("%i - true\n", current_valid_run);}
}
}
// ---------------------------------------------------------------
// Save to file
// ---------------------------------------------------------------
if (time_to_save() || valid_runs == simulation_runs) {
const clock_t now = clock();
const double secs_done = double(now)/CLOCKS_PER_SEC;
const int seconds = int(secs_done) % 60;
const int minutes = int(secs_done / 60) % 60;
const int hours = int(secs_done / 3600) % 24;
const int days = int(secs_done / 86400);
const long percent_done = 100*valid_runs/simulation_runs;
printf("Saving data after %i days, %02i:%02i:%02i, %li iterations (%ld%%) "
"complete.\n", days, hours, minutes, seconds, sw.iteration,
percent_done);
fflush(stdout);
char *countinfo = new char[4096];
sprintf(countinfo,
"# iterations: %li\n"
"# working moves: %li\n"
"# total moves: %li\n"
"# acceptance rate: %g\n"
"# longest failed run: %i\n"
"# longest valid run: %i\n"
"# total checks of small cell: %i\n"
"# total failed small checks: %i\n"
"# total valid small checks: %i\n"
"# valid runs: %i\n"
"# failed runs: %i\n"
"# average valid run: %g\n"
"# average failed run: %g\n\n",
sw.iteration, sw.moves.working, sw.moves.total,
double(sw.moves.working)/sw.moves.total, longest_failed_run,
longest_valid_run, total_checks_of_small_cell, total_failed_small_checks,
total_valid_small_checks, valid_runs, failed_runs, average_valid_run, average_failed_run);
// Save data
if(!sw.walls){
FILE *g_out = fopen((const char *)g_fname, "w");
fprintf(g_out, "%s", headerinfo);
fprintf(g_out, "%s", countinfo);
fclose(g_out);
}
delete[] countinfo;
}
} while (valid_runs < simulation_runs);
// ----------------------------------------------------------------------------
// END OF MAIN PROGRAM LOOP
// ----------------------------------------------------------------------------
for (int i=0; i<sw.N; i++) {
delete[] sw.balls[i].neighbors;
}
delete[] sw.balls;
delete[] sw.ln_energy_weights;
delete[] sw.energy_histogram;
delete[] sw.transitions_table;
delete[] sw.walkers_up;
delete[] sw.pessimistic_observation;
delete[] sw.pessimistic_samples;
delete[] sw.optimistic_samples;
delete[] headerinfo;
delete[] g_fname;
delete[] data_dir;
delete[] filename;
delete[] filename_suffix;
return 0;
}