void initStrain(){
printf("Initializing strain tensor...\n");
//createDeformGradientTensor();
initDeformGradient();
if (stretchOn) initStretch();
atomGreenStrain = (double**)calloc(pdbData.atomCount, sizeof(double*));
int i;
for (i = 0; i < pdbData.atomCount; i++){
atomGreenStrain[i] = (double*)calloc(9, sizeof(double));
}
if (computeOn){
getMaskedParameter(outGreenStrainFilename, "outputGreenStrain", "", 0);
outGreenStrain = fopen(outGreenStrainFilename, "w");
fclose(outGreenStrain);
}
if (printPDBOn){
if (!computeOn){
getMaskedParameter(tnsrGreenStrainFilename, "inputGreenStrain", "", 0);
tnsrGreenStrain = fopen(tnsrGreenStrainFilename, "r");
}
getMaskedParameter(pdbGreenStrainFilename, "outputPDBGreenStrain", "", 0);
pdbGreenStrain = fopen(pdbGreenStrainFilename, "w");
fclose(pdbGreenStrain);
strainNormalScale = getDoubleParameter("strainNormalScaleFactor", 1.0, 1);
strainShearScale = getDoubleParameter("strainShearScaleFactor", 1.0, 1);
}
}
void initSphereStress(){
printf("Initializing sphere stress tensor...\n");
atomSphereStress = (Vector*)calloc(pdbData.atomCount, sizeof(Vector));
if (computeOn){
getMaskedParameter(outSphereStressFilename, "outputSphereStress", "", 0);
outSphereStress = fopen(outSphereStressFilename, "w");
fclose(outSphereStress);
}
if (printPDBOn) {
if (!computeOn){
getMaskedParameter(tnsrSphereStressFilename, "inputSphereStress", "", 0);
tnsrSphereStress = fopen(tnsrSphereStressFilename, "r");
}
getMaskedParameter(pdbSphereStressFilename, "outputPDBSphereStress", "", 0);
pdbSphereStress = fopen(pdbSphereStressFilename, "w");
fclose(pdbSphereStress);
sphereLateralScale = getDoubleParameter("sphereScaleFactor", 1.0, 1);
sphere45ShearScale = getDoubleParameter("sphereScaleFactor", 1.0, 1);
sphereRadialScale = getDoubleParameter("sphereScaleFactor", 1.0, 1);
}
}
int main(int argc, char *argv[])
{
char line[80];
char *xs;
double x;
int which_bin;
int i=0;
instream = stdin;
setCommandLineParameters(argc, argv);
if (getFlagParam("-usage")){
printf("usage: dst2hst -width [1.0]\n");
printf(" -n_bins [64]\n");
printf(" -start_x [0.0]\n");
printf(" \n");
exit(0);
}
while (++i < argc)
{
if ((argc>1) && ((*argv[i]) != '-')) instream = fopen(argv[i], "r");
else if (!strcmp(argv[i], "-width")) width = getDoubleParameter("width", argv[++i]);
else if (!strcmp(argv[i], "-n_bins")) n_bins = getIntParameter("n_bins", argv[++i]);
else if (!strcmp(argv[i], "-start_x")) start_x = getDoubleParameter("start_x", argv[++i]);
}
end_x = start_x + n_bins * width;
while (1)
{
fgets(line, 80, instream);
if (feof(instream)) break;
xs = strtok(line, "\n");
x = strtod(xs, NULL);
if ((x < start_x) || (x > end_x)) fprintf(stderr, "%lf outside of range, discarding...\n", x);
else
{
which_bin = (int)floor((x - start_x)/width);
all_bins[which_bin]++;
}
}
for (which_bin = 0; which_bin<n_bins; which_bin++) printf("%lf\t%d\n", start_x + which_bin*width, all_bins[which_bin]);
}
int main(int argc, char *argv[])
{
int i=0;
double old_energy, new_energy;
double delta_energy;
double boltzmann_factor;
double the_exponential;
int monte_carlo_steps;
int trial_number;
double x0, y0, z0;
double dx, dy, dz;
double rvlen;
double sum_dx, sum_dy, sum_dz;
instream = stdin;
while (++i < argc)
{
if ((argc>1) && (*argv[i] != '-')) instream = fopen(argv[i], "r");
else if (!strcmp(argv[i], "-v")) verbose = 1;
else if (!strcmp(argv[i], "-T")) temperature = getDoubleParameter("temperature", argv[++i]);
else if (!strcmp(argv[i], "-dim"))
{
box_x = getDoubleParameter("box_x", argv[++i]);
box_y = getDoubleParameter("box_y", argv[++i]);
box_z = getDoubleParameter("box_z", argv[++i]);
}
else if (!strcmp(argv[i], "-n_trials")) n_trials = getDoubleParameter("n_trials", argv[++i]);
else if (!strcmp(argv[i], "-rng_seed")) rng_seed = getIntParameter("rng_seed", argv[++i]);
else if (!strcmp(argv[i], "-n_steps")) n_steps = getIntParameter("n_steps", argv[++i]);
else if (!strcmp(argv[i], "-randomize")) rng_seed = getRandomSeed();
else if (!strcmp(argv[i], "-perturbation_length")) perturbation_length = getDoubleParameter("perturbation_length", argv[++i]);
}
initializeRandomNumberGeneratorTo(rng_seed);
loadConfiguration();
for (trial_number = 0; trial_number < n_trials; trial_number++)
{
sum_dx = 0;
sum_dy = 0;
sum_dz = 0;
V printf("trial number %d\n", trial_number);
accepted_moves = 0;
// pick starting point
x0 = x[number_of_molecules] = box_x * rnd();
y0 = y[number_of_molecules] = box_y * rnd();
z0 = z[number_of_molecules] = box_z * rnd();
// move it a bunch of times
for(monte_carlo_steps=0; monte_carlo_steps<n_steps; monte_carlo_steps++)
{
dx = 2*(rnd() - .5);
dy = 2*(rnd() - .5);
dz = 2*(rnd() - .5);
rvlen = perturbation_length / sqrt(dx*dx + dy*dy + dz*dz);
dx *= rvlen;
dy *= rvlen;
dz *= rvlen;
// try out the new position
old_energy = calculateSystemEnergy();
x[number_of_molecules] += dx;
y[number_of_molecules] += dy;
z[number_of_molecules] += dz;
adjustForBoundary(number_of_molecules);
new_energy = calculateSystemEnergy();
delta_energy = new_energy - old_energy;
if (delta_energy <= 0)
{
accepted_moves++;
sum_dx += dx;
sum_dy += dy;
sum_dz += dz;
continue; /* move accepted */
}
the_exponential = 0.0 - delta_energy/temperature;
if (the_exponential > -75)
{
boltzmann_factor = exp(the_exponential);
if (boltzmann_factor > rnd())
{
accepted_moves++;
sum_dx += dx;
sum_dy += dy;
sum_dz += dz;
continue; /* move accepted */
}
}
/* move rejected: */
x[number_of_molecules] -= dx;
y[number_of_molecules] -= dy;
z[number_of_molecules] -= dz;
adjustForBoundary(number_of_molecules);
}
// look at end point, compare
total_translation = sqrt(sum_dx*sum_dx + sum_dy*sum_dy + sum_dz*sum_dz);
printf("%lf\n", total_translation);
V printf("%lf\t%lf\t%lf\t%lf\n", sum_dx, sum_dy, sum_dz, total_translation);
V printf("acceptance ratio: %lf\n", (0.0 + accepted_moves)/n_steps);
}
return 0;
} /* end main */
Control::Control( int argc, char** argv ) {
// parse the command line options to set all vars
if( ( argc % 2 == 0 ) || ( argc == 1 ) ) {
cerr << "Parse error: Number of command line parameters incorrect\n";
cerr << "Usage:" << endl;
cerr << argv[ 0 ] << " -i InputFile [-o OutputFile] [-n NumberOfTries] [-s RandomSeed] [-t TimeLimit] [-p ProblemType]" << endl;
exit(1);
}
for( int i = 1; i < argc / 2 + 1; i++ ) {
parameters[ argv[ i * 2 - 1 ] ] = argv[ i * 2 ];
}
nrTry = 0;
// check for input parameter
if( parameterExists( "-i") ) {
is = new ifstream( getStringParameter( "-i" ).c_str() );
} else {
cerr << "Error: No input file given, exiting" << endl;
cerr << "Usage:" << endl;
cerr << argv[ 0 ] << " -i InputFile [-o OutputFile] [-n NumberOfTries] [-s RandomSeed] [-t TimeLimit] [-p ProblemType]" << endl;
exit(1);
}
// check for ouput parameter
if( parameterExists( "-o" ) ) {
os = new ofstream( getStringParameter( "-o" ).c_str() );
} else {
cerr << "Warning: No output file given, writing to stdout" << endl;
os = &cout;
}
// check for number of tries parameter
if( parameterExists( "-n" ) ) {
maxTry = getIntParameter( "-n" );
cout << "Max number of tries " << maxTry << endl;
} else {
cerr << "Warning: Number of tries is set to default (10)" << endl;
maxTry = 10; // default number of tries
}
// check for time limit parameter
if( parameterExists( "-t" ) ) {
timeLimit = getDoubleParameter( "-t" );
cout <<"Time limit " << timeLimit << endl;
} else {
cerr << "Warning: Time limit is set to default (90 sec)" << endl;
timeLimit = 90; // default time limit
}
// check for problem instance type parameter for the local search
if( parameterExists( "-p" ) ) {
problemType = getIntParameter( "-p" );
cout <<"Problem instance type " << problemType << endl;
} else {
//cerr << "Warning: The problem instance type is set by default to 1 (easy)" << endl;
problemType = 1; // default problem type
}
// check for maximum steps parameter for the local search
if( parameterExists( "-m" ) ) {
maxSteps = getIntParameter( "-m" );
cout <<"Max number of steps in the local search " << maxSteps << endl;
} else {
//cerr << "Warning: The maximum number of steps for the local search is set by default to 100" << endl;
maxSteps = 100; // default max steps
}
// check for time limit parameter for the local search
if( parameterExists( "-l" ) ) {
LS_limit = getDoubleParameter( "-l" );
cout <<"Local search time limit " << LS_limit << endl;
} else {
cerr << "Warning: The local search time limit is set to default (99999 sec)" << endl;
LS_limit = 99999; // default local search time limit
}
// check for probability parameter for each move in the local search
if( parameterExists( "-p1" ) ) {
prob1 = getDoubleParameter( "-p1" );
cout << "LS move 1 probability " << prob1 <<endl;
} else {
cerr << "Warning: The local search move 1 probability is set to default 1.0" << endl;
prob1 = 1.0; // default local search probability for each move of type 1 to be performed
}
if( parameterExists( "-p2" ) ) {
prob2 = getDoubleParameter( "-p2" );
cout <<"LS move 2 probability " << prob2 << endl;
} else {
cerr << "Warning: The local search move 2 probability is set to default 1.0" << endl;
prob2 = 1.0; // default local search probability for each move to be performed
}
if( parameterExists( "-p3" ) ) {
prob3 = getDoubleParameter( "-p3" );
cout <<"LS move 3 probability " << prob3 << endl;
} else {
cerr << "Warning: The local search move 3 probability is set to default 0.0" << endl;
prob3 = 0.0; // default local search probability for each move to be performed
}
// check for random seed
if( parameterExists( "-s" ) ) {
seed = getIntParameter( "-s" );
srand( seed );
} else {
seed = time( NULL );
cerr << "Warning: " << seed << " used as default random seed" << endl;
srand( seed );
}
}
