void print_compaction_score(LinusProtein *p, double cp, char *filename, double *score)
{
FILE *file = fopen(filename,"w+");
//fscanf(file, "%d %s %s %d %s %s Minimum = %lf Actual = %lf\n",i,rn[i],atom->name,j,rn[j],jatm->name, 0.90*(atom->radius+jatm->radius),dist);
fprintf(file,"%s","\n------ Compaction Score -----\n");
double rg = radius_of_gyration(p->atoms,0,p->num_atoms);
fprintf(file,"Radius of Gyration = %lf\n",rg);
fprintf(file,"\nCompaction Score = %lf\n",exp(-rg*rg));
*score = rg*cp;
fclose(file);
}
double compaction_score(LinusProtein *p, double ce)
{
double comp_score;
// ce=1.0
double rg=radius_of_gyration(p->atoms,0,p->num_atoms);
if(rg > ce)
{
comp_score = pow(rg-ce,2.0);
}
else
{
comp_score = 0.0;
}
return comp_score;
}
int main(int argc, char **argv) {
/* the times recorded are:
start of programm, start of chain generation,
end of chain generation, end of programm */
double time[4];
time[0] = time_of_day();
//-----------------------------------------------------------------------------------------------------------------------------------------------
//-----------------------------------------------------------------------------------------------------------------------------------------------
// open all neccessary files
// general output file, contains basically everything which was written to the terminal
FILE * output_file;
output_file = fopen("output_file.dat", "w+");
FILE * conv_obs_file;
conv_obs_file = fopen("convergence_obs.dat", "w+");
// pair correlation function can be weighted with potentials
FILE * pair_correl_file;
pair_correl_file = fopen("pair_correlation_function.dat", "w+");
//------------------------------------------------------------------------------
// all files connected to intramolecular interactions
FILE * intra_pot_file;
intra_pot_file = fopen("intramolecular_obs.dat", "w+");
FILE * intra_boltzman_factors_hist;
intra_boltzman_factors_hist = fopen("intramolecular_factors_hist.dat", "w+");
FILE * intra_interactions_file;
intra_interactions_file = fopen("intramolecular_interactions_hist.dat", "w+");
// FILE * intra_interactions_testfile;
// intra_interactions_testfile = fopen("intramolecular_interactions_testhist.dat", "w+");
FILE * convergence_intraweights;
convergence_intraweights = fopen("intramolecular_convergence_Z.dat", "w+");
fprintf(convergence_intraweights, "### convergence_point -- sum-of-boltzman-factors \n");
FILE * conv_intraobs_file;
conv_intraobs_file = fopen("intramolecular_convergence_obs.dat", "w+");
//-----------------------------------------------------------------------------------------------------------------------------------------------
//-----------------------------------------------------------------------------------------------------------------------------------------------
// input and first output
// hello message of the programm, always displayed!
log_out(output_file, "\n-----------------------------------------------------------------------------------\n");
log_out(output_file, "Roulattice version 1.1, Copyright (C) 2015 Johannes Dietschreit\n");
log_out(output_file, "This program comes with ABSOLUTELY NO WARRANTY; for version details type '-info'.\n");
log_out(output_file, "This is free software, and you are welcome to redistribute it\n");
log_out(output_file, "under certain conditions; type '-license' for details.\n");
log_out(output_file, "\tQuestions and bug reports to: [email protected]\n");
log_out(output_file, "\tPlease include in published work based on Roulattice:\n");
log_out(output_file, "\t\tDietschreit, J. C. B.; Diestler, D. J.; Knapp, E. W.,\n");
log_out(output_file, "\t\tModels for Self-Avoiding Polymer Chains on the Tetrahedral Lattice.\n");
log_out(output_file, "\t\tMacromol. Theory Simul. 2014, 23, 452-463\n");
log_out(output_file, "-----------------------------------------------------------------------------------\n");
/* get the arguments from the comand line */
getArgs(output_file, argc, argv);
//------------------------------------------------------------------------------------
// for reading DCD-files
// this has to be early in the code, because it sets the variables ARG_numberofbeads and ARG_numberofframes!
// variables concerning reading dcd
molfile_timestep_t timestep;
void *v;
dcdhandle *dcd;
int natoms;
float sizeMB =0.0, totalMB = 0.0;
// reading the dcd-file and setting global variables accordingly
if (ARG_typeofrun==0) {
natoms = 0;
v = open_dcd_read(dcdFileName, "dcd", &natoms);
if (!v) {
fprintf(stderr, "ERROR: open_dcd_read failed for file %s\n", dcdFileName);
return EXIT_FAILURE;
}
dcd = (dcdhandle *)v;
sizeMB = ((natoms * 3.0) * dcd->nsets * 4.0) / (1024.0 * 1024.0);
totalMB += sizeMB;
log_out(output_file, "Read DCD: %d atoms, %d frames, size: %6.1fMB\n", natoms, dcd->nsets, sizeMB);
timestep.coords = (float *)malloc(3*sizeof(float)*natoms);
ARG_numberofbeads=dcd->natoms;
ARG_numberofframes=dcd->nsets;
}
//------------------------------------------------------------------------------------
// print all the options to the screen so one can check whether the right thing gets computed
print_set_options(output_file, ARG_typeofrun, ARG_flength, ARG_fflength, ARG_blength, ARG_numberofbeads, ARG_numberofframes, ARG_randomseed, ARG_bondlength, ARG_torsion, ARG_intra_potential, ARG_intra_parameter1, ARG_intra_parameter2);
//-----------------------------------------------------------------------------------------------------------------------------------------------
//-----------------------------------------------------------------------------------------------------------------------------------------------
// physical constants
pi = acos(-1.0);
//-----------------------------------------------------------------------------------------------------------------------------------------------
//-----------------------------------------------------------------------------------------------------------------------------------------------
/* Initialize the most important variables */
// stuff with bond lengths
const double inv_sqrt3 = 1.0/sqrt(3.0);
const double bondlength = ARG_bondlength;
double recast_factor;
if (ARG_typeofrun<40){// this recasts walk on diamond lattice
recast_factor = inv_sqrt3*bondlength;
}
else {// this is for runs on simple cubic lattice
recast_factor = bondlength;
}
// variables with atom numbers etc
const int last_atom = ARG_numberofbeads -1;
const unsigned int number_of_torsions = ARG_numberofbeads -3;
// number of frag, fragfags, endfrags, fragbricks, endbricks
unsigned int numof_frags_bricks[5] = {0};
// fractions of the number of frames
const unsigned long permill_frames = ARG_numberofframes / 1000; // used for convergence
const unsigned long percent_frames = ARG_numberofframes / 100; // used for ramining time
const unsigned long tenth_frames = ARG_numberofframes / 10; // used for error estimation
int cent;
int tenth;
int counter; // counter which can be used at any parts of the main programm, should only be used locally in a loop
// basic moves on the tetrahedral lattice, back and forth
const int move[2][4][3] = {
{
{-1, -1, -1},
{1, 1, -1},
{1, -1, 1},
{-1, 1, 1}
},
{
{1, 1, 1},
{-1, -1, 1},
{-1, 1, -1},
{1, -1, -1}
}
};
// moves possible in SAW (no walking back)
const int sawmoves[4][3] = {
{1, 2, 3},
{0, 2, 3},
{0, 1, 3},
{0, 1, 2}
};
//-----------------------------------------------------------------------
// building bricks are used to put parts together which are pre-checked
int ***building_bricks=NULL;
int numberofbricks;
if (ARG_typeofrun==13 || ARG_typeofrun==14 || ARG_typeofrun==23 || ARG_typeofrun==24 || ARG_typeofrun==33 || ARG_typeofrun==34){
// thise generates the bricks
building_bricks = make_bricks_saw(building_bricks, move, sawmoves, ARG_blength, &numberofbricks, ARG_strictness);
if (NULL==building_bricks[0][0]){
return EXIT_FAILURE;
}
log_out(output_file, "%d bricks were generated, with a length of %d \n", numberofbricks, ARG_blength);
}
//----------------------------------------------------------------------------------------------------------------------------------------------------------
//----------------------------------------------------------------------------------------------------------------------------------------------------------
/* Initialize beads vector and set all values to zero */
int **int_polymer;
int_polymer = calloc(ARG_numberofbeads, sizeof(int *));
double **double_polymer;
double_polymer = calloc(ARG_numberofbeads, sizeof(double *));
for (int dim1=0; dim1<ARG_numberofbeads;dim1++){
int_polymer[dim1] = calloc(3, sizeof(int *));
double_polymer[dim1] = calloc(3, sizeof(double *));
}
//----------------------------------------------------------------------------------------------------------------------------------------------------------
//----------------------------------------------------------------------------------------------------------------------------------------------------------
// observables
OBSERVABLE normal_obs;
normal_obs.maxee = 0.0; // maximal stretch of polymer
OBSERVABLE intra_obs[100];
//-------------------------------------------------------
// initialization of all the OBSERVABLE variables
//-------------------------------------------------------
normal_obs.err_ee2 = (double *) calloc(11, sizeof(double));
if(NULL == normal_obs.err_ee2) {
fprintf(stderr, "Allocation of ee2 variable failed! \n");
return EXIT_FAILURE;
}
normal_obs.err_rgyr = (double *) calloc(11, sizeof(double));
if(NULL == normal_obs.err_rgyr) {
fprintf(stderr, "Allocation of rgyr variable failed! \n");
return EXIT_FAILURE;
}
if (ARG_intra_potential>0) {
for (int dim1=0; dim1<100; dim1++) {
intra_obs[dim1].err_ee2 =(double *) calloc(11, sizeof(double));
intra_obs[dim1].err_rgyr =(double *) calloc(11, sizeof(double));
if(NULL == intra_obs[dim1].err_ee2 || NULL == intra_obs[dim1].err_rgyr) {
fprintf(stderr, "Allocation of ee2 or rgyr variable (intramolecular) failed! \n");
return EXIT_FAILURE;
}
}
}
// initializes the observables for torsional analysis (optional)
if (ARG_torsion==1) {
normal_obs.err_pt = (double *) calloc(11, sizeof(double));
if(NULL == normal_obs.err_pt) {
fprintf(stderr, "Allocation of torsion variable failed! \n");
return EXIT_FAILURE;
}
if (ARG_intra_potential>0) {
for (int dim1=0; dim1<100; dim1++) {
intra_obs[dim1].pt = 0.0;
intra_obs[dim1].err_pt = (double *) calloc(11, sizeof(double));
if(NULL == intra_obs[dim1].err_pt) {
fprintf(stderr, "Allocation of torsion variable (intramolecular) failed! \n");
return EXIT_FAILURE;
}
}
}
}
// initializes the observables for loss of solven accessible surface area analysis (optional)
if (ARG_sasa==1){
normal_obs.err_dsasa = (double *) calloc(11, sizeof(double));
if(NULL == normal_obs.err_dsasa) {
fprintf(stderr, "Allocation of D-SASA variable failed! \n");
return EXIT_FAILURE;
}
if (ARG_intra_potential>0) {
for (int dim1=0; dim1<100; dim1++) {
intra_obs[dim1].dsasa = 0.0;
intra_obs[dim1].err_dsasa = (double *) calloc(11, sizeof(double));
if(NULL == intra_obs[dim1].err_dsasa) {
fprintf(stderr, "Allocation of D-SASA variable (intramolecular) failed! \n");
return EXIT_FAILURE;
}
}
}
}
// this is needed for the pair correlation function
double *pair_correlation_obs;
if (ARG_pair_correlation==1) {
pair_correlation_obs = (double*) calloc(2*ARG_numberofbeads, sizeof(double));
if(NULL == pair_correlation_obs) {
fprintf(stderr, "Allocation of pair_correlation_obs failed! \n");
return EXIT_FAILURE;
}
normal_obs.pair_corr = (double *) calloc(2*ARG_numberofbeads, sizeof(double));
if(NULL == normal_obs.pair_corr) {
fprintf(stderr, "Allocation of pair_corr failed! \n");
return EXIT_FAILURE;
}
if (ARG_intra_potential>0) {
for (int dim1=0; dim1<100; dim1++) {
intra_obs[dim1].pair_corr = (double *) calloc(2*ARG_numberofbeads, sizeof(double));
if(NULL == intra_obs[dim1].pair_corr) {
fprintf(stderr, "Allocation of pair_corr (intramolecular) failed! \n");
return EXIT_FAILURE;
}
}
}
}
//-------------------------
// this will provide a measure for entropy loss calculation
unsigned long *attempts_successes;
double *log_attempts;
log_attempts = (double*) calloc(11, sizeof(double));
// set the number of entries in this list, it depends on the typeofrun, but not the saw-type
// last entry is the recast number of attempts which provides a measure for the entropy loss
//-------------------------------------------------------------------------------------------
//-------------------------------------------------------------------------------------------
// calculate variables which depend on the typeofrun
switch (ARG_typeofrun) {
// normal SAWX
case 10:
case 20:
case 30:
attempts_successes = calloc(2, sizeof(unsigned long));
break;
// fSAWX
case 11:
case 21:
case 31:
attempts_successes = calloc(5, sizeof(unsigned long));
numof_frags_bricks[0] = (ARG_numberofbeads-1)/ARG_flength;
break;
// bSAWX
case 13:
case 23:
case 33:
attempts_successes = calloc(3, sizeof(unsigned long));
numof_frags_bricks[3] = (ARG_numberofbeads-1)/ARG_blength;
break;
// fb_SAWX
case 14:
case 24:
case 34:
attempts_successes = calloc(5, sizeof(unsigned long));
numof_frags_bricks[0] = (ARG_numberofbeads-1)/ARG_flength;
numof_frags_bricks[3] = ARG_flength/ARG_blength;
numof_frags_bricks[4] = (ARG_numberofbeads-1-ARG_flength*numof_frags_bricks[3])/ARG_blength;
break;
default:
break;
}
//----------------------------------------------------------------------------------------------------------------------------------------------------------
//----------------------------------------------------------------------------------------------------------------------------------------------------------
// intra molecular interactions
// boltzman-factors, the intramolecular energy, the enrgy time the boltzmanfactor (entropy)
double *intra_boltzman_factors;
double *intra_highest_boltzmanfactor;
double *intra_energy;
double **intra_sum_of_boltzfactors;
double **intra_sum_of_enrgyboltz;
int *intra_interactions_hist;
// double *intra_interactions_testhist;
double intra_max_factor = 0.0;
double intra_min_factor = 0.0;
// binning the energies of the intra-factors
double intra_binmin;
double intra_binmax;
double intra_binwidth;
int **intra_energybin;
// these will be the parameter of the intra molecular force
double *intra_parameter1;
double *intra_parameter2;
if (ARG_intra_potential > 0){
switch (ARG_intra_potential) {
// 1-10 potential well + torsional potential, given energy values
case 1:
intra_boltzman_factors = (double*) calloc(1, sizeof(double));
intra_highest_boltzmanfactor = (double*) calloc(1, sizeof(double));
intra_energy = (double*) calloc(1, sizeof(double));
intra_sum_of_boltzfactors = (double**) calloc(1, sizeof(double));
intra_sum_of_enrgyboltz = (double**) calloc(1, sizeof(double*));
intra_sum_of_boltzfactors[0] = (double*) calloc(10, sizeof(double));
intra_sum_of_enrgyboltz[0] = (double*) calloc(10, sizeof(double));
intra_parameter1 = (double*) malloc(1 * sizeof(double));
intra_parameter2 = (double*) malloc(1 * sizeof(double));
intra_interactions_hist = calloc(ARG_numberofbeads, sizeof(int));
// intra_interactions_testhist = calloc(100, sizeof(double));
intra_parameter1[0] = ARG_intra_parameter1[0]; // nearest neighbor potential
intra_parameter2[0] = ARG_intra_parameter2[0]; // torsion potential
intra_binmin = -100.0;
intra_binmax = 100.0;
intra_binwidth = 1.0;
intra_energybin = (int**) calloc(1, sizeof(int *));
intra_energybin[0] = (int*) calloc(((intra_binmax-intra_binmin)/intra_binwidth), sizeof(int));
break;
// 1-10 potential well + torsional potential, given energy value range! 10x10
case 2:
intra_boltzman_factors = (double*) calloc(100, sizeof(double));
intra_highest_boltzmanfactor = (double*) calloc(100, sizeof(double));
intra_energy = (double*) calloc(100, sizeof(double));
intra_sum_of_boltzfactors = (double**) calloc(100, sizeof(double));
intra_sum_of_enrgyboltz = (double**) calloc(100, sizeof(double*));
for (int dim1=0; dim1<100; ++dim1) {
intra_sum_of_boltzfactors[dim1] = (double*) calloc(10, sizeof(double));
intra_sum_of_enrgyboltz[dim1] = (double*) calloc(10, sizeof(double));
}
intra_parameter1 = (double*) malloc(10 * sizeof(double));
intra_parameter2 = (double*) malloc(10 * sizeof(double));
intra_interactions_hist = calloc(ARG_numberofbeads, sizeof(int));
// intra_interactions_testhist = calloc(100, sizeof(double));
for (int dim1=0; dim1<10; dim1++) {
intra_parameter1[dim1] = ARG_intra_parameter1[0]+ ARG_intra_parameter1[1]*(double)dim1; // nearest neighbor potential
intra_parameter2[dim1] = ARG_intra_parameter2[0]+ ARG_intra_parameter2[1]*(double)dim1; // torsion potential
}
intra_binmin = -100.0;
intra_binmax = 100.0;
intra_binwidth = 1.0;
intra_energybin = (int**) calloc(100, sizeof(int *));
for (int dim1=0; dim1<100; ++dim1){
intra_energybin[dim1] = (int*) calloc(((intra_binmax-intra_binmin)/intra_binwidth), sizeof(int));
}
break;
default:
fprintf(stderr, "This intramolecular potential doesn't exist! \n");
break;
}
}
//----------------------------------------------------------------------------------------------------------------------------------------------------------
//----------------------------------------------------------------------------------------------------------------------------------------------------------
/* start of chain generation*/
time[1] = time_of_day();
for (unsigned long frame=0; frame<ARG_numberofframes; frame++){
tenth = frame/tenth_frames;
switch(ARG_typeofrun){
case 0:
dcd_to_polymer(double_polymer, v, natoms, ×tep, dcd, frame, ARG_numberofbeads);
break;
case 1:
tetra_rw(int_polymer, move, ARG_numberofbeads);
break;
case 2:
tetra_fww(int_polymer, move, sawmoves, ARG_numberofbeads);
break;
case 10:
tetra_saw1(int_polymer, move, sawmoves, ARG_numberofbeads, attempts_successes);
break;
case 11:
tetra_fsaw1(int_polymer, move, sawmoves, ARG_numberofbeads, ARG_flength, attempts_successes);
break;
case 13:
tetra_bsaw1(int_polymer, move, sawmoves, ARG_numberofbeads, ARG_blength, numberofbricks, building_bricks, attempts_successes);
break;
// case 14: // here is something awfully wrong, can't find the mistake at the moment!
// tetra_fb_saw1(int_polymer, move, sawmoves, ARG_numberofbeads, ARG_blength, numberofbricks, building_bricks, ARG_flength, attempts_successes);
// break;
case 20:
tetra_saw2(int_polymer, move, sawmoves, ARG_numberofbeads, attempts_successes);
break;
case 21:
tetra_fsaw2(int_polymer, move, sawmoves, ARG_numberofbeads, ARG_flength, attempts_successes);
break;
case 23:
tetra_bsaw2(int_polymer, move, sawmoves, ARG_numberofbeads, ARG_blength, numberofbricks, building_bricks, attempts_successes);
break;
case 24:
tetra_fb_saw2(int_polymer, move, sawmoves, ARG_numberofbeads, ARG_blength, numberofbricks, building_bricks, ARG_flength, attempts_successes);
break;
case 30:
tetra_saw3(int_polymer, move, sawmoves, ARG_numberofbeads, attempts_successes);
break;
case 31:
tetra_fsaw3(int_polymer, move, sawmoves, ARG_numberofbeads, ARG_flength, attempts_successes);
break;
case 33:
tetra_bsaw3(int_polymer, move, sawmoves, ARG_numberofbeads, ARG_blength, numberofbricks, building_bricks, attempts_successes);
break;
case 34:
tetra_fb_saw3(int_polymer, move, sawmoves, ARG_numberofbeads, ARG_blength, numberofbricks, building_bricks, ARG_flength, attempts_successes);
break;
default:
log_out(output_file, "ERROR: ARG_typeofrun = %d isn't recognized by the main part of the programm!\n", ARG_typeofrun);
usage_error();
} // end of chain generaiton
// copies the lattice polymer into an array with doubles so that the chosen bond length can be used.
if (ARG_typeofrun>0) {
recast(double_polymer, int_polymer, ARG_numberofbeads, &recast_factor);
}
//-----------------------------------------------------------------------------
//-----------------------------------------------------------------------------
// get most important observables
// end-to-end distance^2
normal_obs.ee2 = double_distance2(double_polymer[last_atom], double_polymer[0]);
normal_obs.err_ee2[tenth] += normal_obs.ee2;
// radius of gyration
normal_obs.rgyr = radius_of_gyration(double_polymer, ARG_numberofbeads);
normal_obs.err_rgyr[tenth] += normal_obs.rgyr;
// pT
if (ARG_torsion==1){
normal_obs.pt = get_nT(double_polymer, number_of_torsions);
normal_obs.err_pt[tenth] += normal_obs.pt;
}
if (ARG_sasa==1){
//observables[4] = get_asa(double_polymer, ARG_numberofbeads, (sqrt(16.0/3.0)*bondlength/2.0));
normal_obs.dsasa = delta_asa(double_polymer, ARG_numberofbeads, bondlength);
normal_obs.err_dsasa[tenth] += normal_obs.dsasa;
}
if (ARG_pair_correlation==1) {
if (false==pair_correlation_fct(pair_correlation_obs, double_polymer, ARG_numberofbeads)){
return EXIT_FAILURE;
}
for (int pairs=0; pairs<(2*ARG_numberofbeads); pairs++) {
normal_obs.pair_corr[pairs] += pair_correlation_obs[pairs];
}
}
//-----------------------------------------------------------------------------
//-----------------------------------------------------------------------------
// calculate boltzman factors if intramolecular forces are switched on
switch (ARG_intra_potential) {
// torsion + square well potential
case 1:
intrapot_torsion_well(intra_boltzman_factors, intra_energy, intra_interactions_hist, intra_highest_boltzmanfactor, intra_parameter1, intra_parameter2, normal_obs.pt, number_of_torsions, int_polymer, ARG_numberofbeads);
intra_sum_of_enrgyboltz[0][tenth] += (intra_boltzman_factors[0]*intra_energy[0]);
intra_sum_of_boltzfactors[0][tenth] += intra_boltzman_factors[0];
intra_obs[0].err_ee2[tenth] += normal_obs.ee2 * intra_boltzman_factors[0];
intra_obs[0].err_rgyr[tenth] += normal_obs.rgyr * intra_boltzman_factors[0];
intra_obs[0].err_pt[tenth] += normal_obs.pt * intra_boltzman_factors[0];
intra_binenergy(intra_energy[0], intra_binmin, intra_binwidth, intra_energybin[0]);
// pair correlation function
if (ARG_pair_correlation==1){
for (int pairs=0; pairs<(2*ARG_numberofbeads); pairs++) {
intra_obs[0].pair_corr[pairs] += (pair_correlation_obs[pairs]*intra_boltzman_factors[0]);
}
}
break;
// torsion + square well potential, range of energy values
case 2:
intrapot_torsion_well_scan(intra_boltzman_factors, intra_energy, intra_interactions_hist, intra_highest_boltzmanfactor, intra_parameter1, intra_parameter2, normal_obs.pt, number_of_torsions, int_polymer, ARG_numberofbeads);
//intrapot_torsion_well_test(intra_boltzman_factors, intra_energy, intra_interactions_hist, intra_interactions_testhist,intra_highest_boltzmanfactor, intra_parameter1, intra_parameter2, normal_obs.pt, number_of_torsions, int_polymer, ARG_numberofbeads);
for (int dim1=0; dim1<100; ++dim1) {
intra_sum_of_enrgyboltz[dim1][tenth] += (intra_boltzman_factors[dim1]*intra_energy[dim1]);
intra_sum_of_boltzfactors[dim1][tenth] += intra_boltzman_factors[dim1];
intra_obs[dim1].err_ee2[tenth] += normal_obs.ee2 * intra_boltzman_factors[dim1];
intra_obs[dim1].err_rgyr[tenth] += normal_obs.rgyr * intra_boltzman_factors[dim1];
intra_obs[dim1].err_pt[tenth] += normal_obs.pt * intra_boltzman_factors[dim1];
intra_binenergy(intra_energy[dim1], intra_binmin, intra_binwidth, intra_energybin[dim1]);
// pair correlation function
if (ARG_pair_correlation==1){
for (int pairs=0; pairs<(2*ARG_numberofbeads); pairs++) {
intra_obs[dim1].pair_corr[pairs] += (pair_correlation_obs[pairs]*intra_boltzman_factors[dim1]);
}
}
}
break;
default:
break;
}// boltzman factors and energies have been determined
// end of anything related to intramolecular potentials
//--------------------------------------------------------------------------------------------
//--------------------------------------------------------------------------------------------
// everything has been calculated, now is the opportunity to look at convergence
if ((frame+1)%permill_frames==0) {
// convergence of variables with equal weights
convergence(&normal_obs, (double)number_of_torsions, (frame+1), conv_obs_file);
switch (ARG_intra_potential) {
case 1:
weighted_convergence(intra_obs, 1,intra_sum_of_boltzfactors, (double)number_of_torsions, (frame+1), conv_intraobs_file);
weights_growth(intra_sum_of_boltzfactors, 1, (frame+1), convergence_intraweights);
break;
// convergence of weighted ensemble
case 2:
weighted_convergence(intra_obs, 100, intra_sum_of_boltzfactors, (double)number_of_torsions, (frame+1), conv_intraobs_file);
weights_growth(intra_sum_of_boltzfactors, 100, (frame+1), convergence_intraweights);
break;
default:
break;
}
if ((frame+1)%percent_frames==0) {
cent = (frame+1)/percent_frames;
log_out(output_file, "Finished %i%%\t...remaining time: %f seconds \n", (cent), ((time_of_day()-time[1])*(100-cent)/(cent)));
if ((frame+1)%tenth_frames==0) {
// every bin after the first will also include the attempts in the previous bin!
log_attempts[tenth] = recalc_attempts(attempts_successes, numof_frags_bricks, numberofbricks, ARG_typeofrun);
}
}
}
} // end of loop over number of frames
//----------------------------------------------------------------------------------------------------------------------------------------------------------
//----------------------------------------------------------------------------------------------------------------------------------------------------------
/* Post-Process */
time[2] = time_of_day();
// Maybe there should be a function, which returns means and errors; it calls these subroutines ....
log_attempts[10] = recalc_attempts(attempts_successes, numof_frags_bricks, numberofbricks, ARG_typeofrun);
for (int dim1=9; dim1>0; --dim1) {
log_attempts[dim1] = log( exp(log_attempts[dim1]) - exp(log_attempts[dim1-1]) );
}
// get means and errors
normal_obs.ee2 = sqrt( average(normal_obs.err_ee2, ARG_numberofframes) );
normal_obs.err_ee2[10] = error_sq_ten(normal_obs.ee2, normal_obs.err_ee2, ARG_numberofframes);
normal_obs.rgyr = sqrt( average(normal_obs.err_rgyr, ARG_numberofframes) );
normal_obs.err_rgyr[10] = error_sq_ten(normal_obs.rgyr, normal_obs.err_rgyr, ARG_numberofframes);
normal_obs.S = (log((double)ARG_numberofframes) - log_attempts[10]);
if (ARG_torsion==1) {
normal_obs.pt = average(normal_obs.err_pt, ARG_numberofframes);
normal_obs.err_pt[10] = error_ten(normal_obs.pt, normal_obs.err_pt, ARG_numberofframes);
}
if (ARG_sasa==1) {
normal_obs.dsasa = average(normal_obs.err_dsasa, ARG_numberofframes);
normal_obs.err_dsasa[10] = error_ten(normal_obs.dsasa, normal_obs.err_dsasa, ARG_numberofframes);
}
//----------------------------------------------------------------------------------------------------------------------------------------------------------
//----------------------------------------------------------------------------------------------------------------------------------------------------------
/* Output */
time[3] = time_of_day();
// print the output to screen and to the output_file
log_out(output_file, "\n-----------------------------------------------------------------------------------\n");
log_out(output_file, "FINAL OUTPUT\n");
log_out(output_file, "\nEntropic Considerations:\n");
log_out(output_file, "Attempts to Compute the Ensemble: %e \n", exp(log_attempts[10]));
log_out(output_file, "\tDelta S / k_B (FWW -> SAWn): %f \n", normal_obs.S);
log_out(output_file, "\nChosen Observables:\n");
log_out(output_file, "Flory Radius: %f +- %f \n", normal_obs.ee2, normal_obs.err_ee2[10]);
log_out(output_file, "Radius of Gyration: %f +- %f \n", normal_obs.rgyr, normal_obs.err_rgyr[10]);
if (ARG_torsion==1) {
log_out(output_file, "Probability of trans = %f +- %f\n", (normal_obs.pt/(double)number_of_torsions), (normal_obs.err_pt[10]/(double)number_of_torsions));
}
if (ARG_sasa==1) {
log_out(output_file, "Delta SASA = %f +- %f\n", normal_obs.dsasa, normal_obs.err_dsasa[10]);
}
if (ARG_pair_correlation==1) {
log_out(output_file, "The pair-correlation function was written to 'pair_correlation_function.dat'.\n");
}
log_out(output_file, "\nThis ouput is also written to 'output_file.dat'.\n");
log_out(output_file, "The convergence was written to 'convergence_obs.dat'.\n");
if (ARG_intra_potential>0) {
log_out(output_file, "\nThe Boltzmann-weighted observables can be found in 'intramolecular_obs.dat'.\n");
log_out(output_file, "The Boltzmann-weighted convergence was written to 'intramolecular_convergence_obs.dat'.\n");
log_out(output_file, "A histogram of the Boltzmann-factors was written to 'intramolecular_factors_hist.dat'.\n");
log_out(output_file, "The sum of the Boltzmann-factors was written to 'intramolecular_convergence_Z.dat'.\n");
log_out(output_file, "A histogram of the intramolecular contacts was written to 'intramolecular_interactions_hist.dat'.\n");
}
//----------------------------------------------------------------------------------------------------------------------------------------------------------
//----------------------------------------------------------------------------------------------------------------------------------------------------------
/* Output to file */
// pair correlation function
if (ARG_pair_correlation==1){
if (ARG_intra_potential==0) {
fprintf(pair_correl_file,"# r_0-r_1 pair_correlation \n");
for (int dim1=0; dim1<(2*ARG_numberofbeads); dim1++){
fprintf(pair_correl_file, "%i %e \n", dim1, (normal_obs.pair_corr[dim1]/(double)ARG_numberofframes));
}
}
else if (ARG_intra_potential==2){
fprintf(pair_correl_file,"# r_0-r_1 pair_correlation(unweigthed) pair_correlation(weigthed)\n");
for (int dim1=0; dim1<(2*ARG_numberofbeads); dim1++){
fprintf(pair_correl_file, "%i %e %e \n", dim1, (normal_obs.pair_corr[dim1]/(double)ARG_numberofframes), (intra_obs[46].pair_corr[dim1]/average(intra_sum_of_boltzfactors[46], 1)));
}
}
}
switch (ARG_intra_potential) {
case 1:
// prints the weighted observables to file with error estimate
fprintf(intra_pot_file, "### 1-9 well, torsion eps, Rf, Rf_err, Rg, Rg_err, pT, pT_err, DS, DS_err, <exp(-E/kT)>/exp(-Emax/kT) \n" );
intra_obs[0].ee2 = sqrt(weighted_average(intra_obs[0].err_ee2, intra_sum_of_boltzfactors[0]));
intra_obs[0].err_ee2[10] = weighted_error_sq_ten(intra_obs[0].ee2, intra_obs[0].err_ee2, intra_sum_of_boltzfactors[0]);
intra_obs[0].rgyr = sqrt(weighted_average(intra_obs[0].err_rgyr, intra_sum_of_boltzfactors[0]));
intra_obs[0].err_rgyr[10] = weighted_error_sq_ten(intra_obs[0].rgyr, intra_obs[0].err_rgyr, intra_sum_of_boltzfactors[0]);
intra_obs[0].pt = weighted_average(intra_obs[0].err_pt, intra_sum_of_boltzfactors[0]);
intra_obs[0].err_pt[10] = weighted_error_ten(intra_obs[0].pt, intra_obs[0].err_pt, intra_sum_of_boltzfactors[0]);
intra_obs[0].S = intra_entropy(intra_sum_of_boltzfactors[0], intra_sum_of_enrgyboltz[0], log_attempts[10]);
intra_obs[0].err_S = intra_entropy_error_ten(intra_obs[0].S, intra_sum_of_boltzfactors[0], intra_sum_of_enrgyboltz[0], log_attempts);
fprintf(intra_pot_file, "%f %f %e %e %e %e %e %e %e %e %e \n", intra_parameter1[0], intra_parameter2[0], intra_obs[0].ee2, intra_obs[0].err_ee2[10], intra_obs[0].rgyr, intra_obs[0].err_rgyr[10], (intra_obs[0].pt/(double)number_of_torsions), (intra_obs[0].err_pt[10]/(double)number_of_torsions), intra_obs[0].S, intra_obs[0].err_S, intra_loss_of_conf(intra_sum_of_boltzfactors[0], intra_highest_boltzmanfactor[0], ARG_numberofframes));
// histogram over 1-9 interacitons
fprintf(intra_interactions_file, "# number-of-nn-interactions, occurence \n");
for (int dim1=0; dim1<ARG_numberofbeads; ++dim1) {
fprintf(intra_interactions_file, "%i %i \n", dim1, intra_interactions_hist[dim1]);
}
// test histogram
// fprintf(intra_interactions_testfile, "# sperating-bonds 0_contacts 1_contacts 2_contacts\n");
// for (int dim1=0; dim1<98; dim1+=3) {
// fprintf(intra_interactions_testfile, "%i %e %e %e \n", (dim1/3+4), intra_interactions_testhist[dim1]/average(intra_sum_of_boltzfactors[46], 1), intra_interactions_testhist[dim1+1]/average(intra_sum_of_boltzfactors[46], 1), intra_interactions_testhist[dim1+2]/average(intra_sum_of_boltzfactors[46], 1));
// }
// histogram of intra energies
fprintf(intra_boltzman_factors_hist, "# energy, bincount-for-these-parameters");
for (int dim1=0; dim1<((intra_binmax-intra_binmin)/intra_binwidth); ++dim1) {
fprintf(intra_boltzman_factors_hist, "%f %i \n", (intra_binmin+(double)dim1*intra_binwidth), intra_energybin[0][dim1]);
}
break;
case 2:
// prints the weighted observables to file with error estimate
fprintf(intra_pot_file, "### 1-9 well, torsion eps, Rf, Rf_err, Rg, Rg_err, pT, pT_err, DS, DS_err, <exp(-E/kT)>/exp(-Emax/kT) \n" );
for (int dim1=0; dim1<10; dim1++) {
for (int dim2=0; dim2<10; dim2++) {
counter = dim1*10 + dim2;
intra_obs[counter].ee2 = sqrt(weighted_average(intra_obs[counter].err_ee2, intra_sum_of_boltzfactors[counter]));
intra_obs[counter].err_ee2[10] = weighted_error_sq_ten(intra_obs[counter].ee2, intra_obs[counter].err_ee2, intra_sum_of_boltzfactors[counter]);
intra_obs[counter].rgyr = sqrt(weighted_average(intra_obs[counter].err_rgyr, intra_sum_of_boltzfactors[counter]));
intra_obs[counter].err_rgyr[10] = weighted_error_sq_ten(intra_obs[counter].rgyr, intra_obs[counter].err_rgyr, intra_sum_of_boltzfactors[counter]);
intra_obs[counter].pt = weighted_average(intra_obs[counter].err_pt, intra_sum_of_boltzfactors[counter]);
intra_obs[counter].err_pt[10] = weighted_error_ten(intra_obs[counter].pt, intra_obs[counter].err_pt, intra_sum_of_boltzfactors[counter]);
intra_obs[counter].S = intra_entropy(intra_sum_of_boltzfactors[counter], intra_sum_of_enrgyboltz[counter], log_attempts[10]);
intra_obs[counter].err_S = intra_entropy_error_ten(intra_obs[counter].S, intra_sum_of_boltzfactors[counter], intra_sum_of_enrgyboltz[counter], log_attempts);
fprintf(intra_pot_file, "%f %f %e %e %e %e %e %e %e %e %e \n", intra_parameter1[dim1], intra_parameter2[dim2], intra_obs[counter].ee2, intra_obs[counter].err_ee2[10], intra_obs[counter].rgyr, intra_obs[counter].err_rgyr[10], (intra_obs[counter].pt/(double)number_of_torsions), (intra_obs[counter].err_pt[10]/(double)number_of_torsions), intra_obs[counter].S, intra_obs[counter].err_S, intra_loss_of_conf(intra_sum_of_boltzfactors[counter], intra_highest_boltzmanfactor[counter], ARG_numberofframes));
}
}
// histogram over 1-9 interacitons
fprintf(intra_interactions_file, "# number-of-nn-interactions, occurence \n");
for (int dim1=0; dim1<ARG_numberofbeads; ++dim1) {
fprintf(intra_interactions_file, "%i %i \n", dim1, intra_interactions_hist[dim1]);
}
// test histogram
// fprintf(intra_interactions_testfile, "# sperating-bonds 0_contacts 1_contacts 2_contacts\n");
// for (int dim1=0; dim1<98; dim1+=3) {
// fprintf(intra_interactions_testfile, "%i %e %e %e \n", (dim1/3+4), intra_interactions_testhist[dim1]/average(intra_sum_of_boltzfactors[46], 1), intra_interactions_testhist[dim1+1]/average(intra_sum_of_boltzfactors[46], 1), intra_interactions_testhist[dim1+2]/average(intra_sum_of_boltzfactors[46], 1));
// }
// histogram of intra energies
fprintf(intra_boltzman_factors_hist, "# energy, bincount-for-these-parameters");
for (int dim1=0; dim1<((intra_binmax-intra_binmin)/intra_binwidth); ++dim1) {
fprintf(intra_boltzman_factors_hist, "%f ", (intra_binmin+(double)dim1*intra_binwidth));
for (int dim2=0; dim2<100; ++dim2) {
fprintf(intra_boltzman_factors_hist, "%i ", intra_energybin[dim2][dim1]);
}
fprintf(intra_boltzman_factors_hist, "\n");
}
break;
default:
break;
}
log_out(output_file, "\nComputation of Chains:\t%f seconds \nTotal Runtime:\t\t%f seconds \n\n", (time[2]-time[1]), (time[3]-time[0]));
log_out(output_file, "End of Programm!\n-----------------------------------------------------------------------------------\n");
// make sure everything gets printed
fflush(stdout);
//----------------------------------------------------------------------------------------------------------------------------------------------------------
//----------------------------------------------------------------------------------------------------------------------------------------------------------
// close every remaining file and free remaining pointers!
// cleaning up ;-)
//close all files
if (ARG_typeofrun==0){// dcd-file
close_file_read(v);
}
fclose(conv_obs_file);
fclose(pair_correl_file);
fclose(intra_pot_file);
fclose(intra_boltzman_factors_hist);
fclose(convergence_intraweights);
fclose(intra_interactions_file);
fclose(conv_intraobs_file);
// very last file to close
fclose(output_file);
//-----------------------------
// free pointers
// free general variables
free(normal_obs.err_ee2);
free(normal_obs.err_rgyr);
// torsion angles
if (ARG_torsion==1) {
free(normal_obs.err_pt);
if (ARG_intra_potential>0) {
for (int dim1=0; dim1<100; dim1++) {
free(intra_obs[dim1].err_pt);
}
}
}
// D-SASA
if (ARG_sasa==1) {
free(normal_obs.err_dsasa);
if (ARG_intra_potential>0) {
for (int dim1=0; dim1<100; dim1++) {
free(intra_obs[dim1].err_dsasa);
}
}
}
// pair correlation function
if (ARG_pair_correlation==1) {
free(pair_correlation_obs);
free(normal_obs.pair_corr);
if (ARG_intra_potential>0) {
for (int dim1=0; dim1<100; dim1++) {
free(intra_obs[dim1].pair_corr);
}
}
}
free(attempts_successes);
// free arrays which held polymer coordinates
for (int dim1=0; dim1<ARG_numberofbeads;dim1++){
free(int_polymer[dim1]);
free(double_polymer[dim1]);
}
free(int_polymer);
free(double_polymer);
// free building blocks
if (ARG_typeofrun==13 || ARG_typeofrun==14 || ARG_typeofrun==23 || ARG_typeofrun==24 || ARG_typeofrun==33 || ARG_typeofrun==34){
for (int dim1=0; dim1<numberofbricks; ++dim1) {
for (int dim2=0; dim2<ARG_blength; ++dim2) {
free(building_bricks[dim1][dim2]);
}
free(building_bricks[dim1]);
}
free(building_bricks);
}
// free potential variables
if (ARG_intra_potential > 0){
switch (ARG_intra_potential) {
case 1:
free(intra_sum_of_boltzfactors[0]);
break;
case 2:
for (int dim1=0; dim1<100; dim1++){
free(intra_sum_of_boltzfactors[dim1]);
}
break;
default:
break;
}
free(intra_energy);
free(intra_boltzman_factors);
free(intra_sum_of_boltzfactors);
free(intra_sum_of_enrgyboltz);
free(intra_interactions_hist);
// free(intra_interactions_testhist);
free(intra_parameter1);
free(intra_parameter2);
}
// end of programm
return EXIT_SUCCESS;
}