void HttpRequest::answer ( const shared_ptr<Tile>& tile, Reply::StatusType status )
{
if (checkifAnswered()) return;
reply.status = status;
reply.content = "";
reply.tile = tile;
reply.headers.resize ( 2 );
reply.headers[0].name = "Content-Length";
reply.headers[0].value = boost::lexical_cast<string> ( tile->getImage()->size() );
reply.headers[1].name = "Content-Type";
reply.headers[1].value = "image/";
reply.headers[1].value.append ( tile->getIdentifier()->getImageFormatString() );
// IP Date Method url Version Reply Size duration
//80.101.90.180 - [02/Jun/2009:15:11:52 -0400] "GET /css/style.css HTTP/1.1" 200 2816 12
auto now = boost::posix_time::second_clock::local_time();
LOG_SEV(access_log, info) << socket.remote_endpoint().address().to_string()
<< " - ["
<< now.date().day() << "/" << now.date().month() << "/" << now.date().year()
<< ":" << now.time_of_day().hours() << ":" << now.time_of_day().minutes() << ":" << now.time_of_day().seconds()
<< "] \""
<< data.method << " " << data.uri << " HTTP/" << data.http_version_major << "." << data.http_version_minor << "\" "
<< reply.status << " " << reply.headers[0].value;
LOG_SEV(server_log, info) << "Answered \"" << data.uri << "\"";
answer();
}
std::string timestamp_str()
{
const auto now = boost::posix_time::second_clock::local_time();
char buf[2048];
sprintf(buf, "on %04d-%02d-%02d at %02d:%02d:%02d",
// Local date in an ANSII format.
int(now.date().year()), int(now.date().month()), int(now.date().day()),
int(now.time_of_day().hours()), int(now.time_of_day().minutes()), int(now.time_of_day().seconds()));
return buf;
}
void time_of_day::parse_times(const config& cfg, std::vector<time_of_day>& times)
{
for(const config &t : cfg.child_range("time")) {
times.push_back(time_of_day(t));
}
if(times.empty())
{
// Make sure we have at least default time
times.push_back(time_of_day());
}
}
void time_of_day::parse_times(const config& cfg, std::vector<time_of_day>& normal_times)
{
BOOST_FOREACH(const config &t, cfg.child_range("time")) {
normal_times.push_back(time_of_day(t));
}
if(normal_times.empty())
{
// Make sure we have at least default time
normal_times.push_back(time_of_day());
}
}
void time_of_day::parse_times(const config& cfg, std::vector<time_of_day>& normal_times)
{
foreach (const config &t, cfg.child_range("time")) {
normal_times.push_back(time_of_day(t));
}
if(normal_times.empty())
{
// Make sure we have at least default time
config dummy_cfg;
normal_times.push_back(time_of_day(dummy_cfg));
}
}
void FPS::prepare() {
if (!displayed()) return;
++loop_count;
double curtime = time_of_day();
// force a redraw....
need_matrix_recalc();
// but don't redraw indicator more than twice per second
if (curtime - last_update < 0.5) return;
double rate = loop_count / (curtime - last_update);
last_update = curtime;
loop_count = 0;
reset_disp_list();
append(DMATERIALOFF);
float asp = disp->aspect();
float poscale = 1.2f;
float pos[3];
pos[0] = asp * poscale;
pos[1] = poscale;
pos[2] = 0;
DispCmdColorIndex cmdColor;
cmdColor.putdata(usecolor, cmdList);
DispCmdText cmdText;
char buf[20];
sprintf(buf, "%5.2f", rate);
cmdText.putdata(pos, buf, 1.0f, cmdList);
}
string get_time_string_s_file()
{
auto tm = boost::posix_time::microsec_clock::local_time();
auto date = tm.date();
auto time = tm.time_of_day();
char buff[32];
sprintf_s(buff, "%u-%02u-%02u %02u.%02u.%02u", (int)date.year(), (int)date.month(), (int)date.day(), \
(int)time.hours(), (int)time.minutes(), (int)time.seconds());
return buff;
}
int main(int argc, char *argv[]) {
molfile_timestep_t timestep;
void *v;
jshandle *js;
int i, natoms;
float sizeMB =0.0, totalMB = 0.0;
double starttime, endtime, totaltime = 0.0;
while (--argc) {
++argv;
natoms = 0;
v = open_js_read(*argv, "js", &natoms);
if (!v) {
printf("jsplugin) open_js_read failed for file %s\n", *argv);
return 1;
}
js = (jshandle *)v;
sizeMB = ((natoms * 3.0) * js->nframes * 4.0) / (1024.0 * 1024.0);
totalMB += sizeMB;
printf("jsplugin) file: %s\n", *argv);
printf("jsplugin) %d atoms, %d frames, size: %6.1fMB\n", natoms, js->nframes, sizeMB);
starttime = time_of_day();
timestep.coords = (float *)malloc(3*sizeof(float)*natoms);
for (i=0; i<js->nframes; i++) {
int rc = read_js_timestep(v, natoms, ×tep);
if (rc) {
printf("jsplugin) error in read_js_timestep on frame %d\n", i);
return 1;
}
}
endtime = time_of_day();
close_js_read(v);
totaltime += endtime - starttime;
printf("jsplugin) Time: %5.1f seconds\n", endtime - starttime);
printf("jsplugin) Speed: %5.1f MB/sec, %5.1f timesteps/sec\n", sizeMB / (endtime - starttime), (js->nframes / (endtime - starttime)));
}
printf("jsplugin) Overall Size: %6.1f MB\n", totalMB);
printf("jsplugin) Overall Time: %6.1f seconds\n", totaltime);
printf("jsplugin) Overall Speed: %5.1f MB/sec\n", totalMB / totaltime);
return 0;
}
int main(int argc, char *argv[]) {
molfile_timestep_t timestep;
void *v;
dcdhandle *dcd;
int i, natoms;
float sizeMB =0.0, totalMB = 0.0;
double starttime, endtime, totaltime = 0.0;
while (--argc) {
++argv;
natoms = 0;
v = open_dcd_read(*argv, "dcd", &natoms);
if (!v) {
fprintf(stderr, "main) open_dcd_read failed for file %s\n", *argv);
return 1;
}
dcd = (dcdhandle *)v;
sizeMB = ((natoms * 3.0) * dcd->nsets * 4.0) / (1024.0 * 1024.0);
totalMB += sizeMB;
printf("main) file: %s\n", *argv);
printf(" %d atoms, %d frames, size: %6.1fMB\n", natoms, dcd->nsets, sizeMB);
starttime = time_of_day();
timestep.coords = (float *)malloc(3*sizeof(float)*natoms);
for (i=0; i<dcd->nsets; i++) {
int rc = read_next_timestep(v, natoms, ×tep);
if (rc) {
fprintf(stderr, "error in read_next_timestep on frame %d\n", i);
return 1;
}
}
endtime = time_of_day();
close_file_read(v);
totaltime += endtime - starttime;
printf(" Time: %5.1f seconds\n", endtime - starttime);
printf(" Speed: %5.1f MB/sec, %5.1f timesteps/sec\n", sizeMB / (endtime - starttime), (dcd->nsets / (endtime - starttime)));
}
printf("Overall Size: %6.1f MB\n", totalMB);
printf("Overall Time: %6.1f seconds\n", totaltime);
printf("Overall Speed: %5.1f MB/sec\n", totalMB / totaltime);
return 0;
}
int TclTextInterp::done_waiting() {
if (delay > 0) {
double elapsed = time_of_day() - starttime;
if (elapsed > delay) {
delay = -1; // done waiting
} else {
return 0; // not done yet
}
}
return 1; // done
}
void editor_controller::init_tods(const config& game_config)
{
const config &cfg = game_config.child("editor_times");
if (!cfg) {
ERR_ED << "No editor time-of-day defined\n";
return;
}
foreach (const config &i, cfg.child_range("time")) {
tods_.push_back(time_of_day(i));
}
}
void custom_tod::do_delete_tod(window& window)
{
assert(tods_.begin() + current_tod_ < tods_.end());
if(tods_.size() == 1) {
tods_.at(0) = time_of_day();
update_selected_tod_info(window);
return;
}
tods_.erase(tods_.begin() + current_tod_);
if(tods_.begin() + current_tod_ >= tods_.end()) {
current_tod_ = tods_.size() - 1;
}
update_selected_tod_info(window);
}
/// And now the class definition
VMDTitle::VMDTitle(DisplayDevice *d, Displayable *par)
: Displayable(par), disp(d) {
// displayable characteristics
rot_off();
scale_off();
glob_trans_off();
cent_trans_off();
letterson = TRUE;
redraw_list();
glob_trans_on();
set_glob_trans(0, 0.5, 0);
glob_trans_off();
starttime = time_of_day();
}
FPS::FPS(DisplayDevice *d, Displayable *par)
: Displayable(par), disp(d) {
last_update = time_of_day(); // setup time of day with initial value
loop_count = 0;
// disable transformations on this displayable
rot_off();
glob_trans_off();
cent_trans_off();
scale_off();
// set the text color category, index, etc.
colorCat = scene->add_color_category("Display");
if (colorCat < 0)
colorCat = scene->category_index("Display");
usecolor = scene->add_color_item(colorCat, "FPS", REGWHITE);
do_color_changed(colorCat);
}
void custom_tod::do_new_tod(window& window)
{
tods_.insert(tods_.begin() + current_tod_, time_of_day());
update_selected_tod_info(window);
}
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;
}
void TclTextInterp::wait(float wd) {
delay = wd;
starttime = time_of_day();
}
time_type operator+=(const date_duration_type& dd)
{
time_ = (time_system::get_time_rep(date() + dd, time_of_day()));
return time_type(time_);
}
void VMDTitle::prepare() {
double elapsed = time_of_day() - starttime;
double delta;
// Prevent the title screen from hogging the CPU/GPU when there's
// nothing else going on. This is particularly important for users
// that start VMD and immediately start using Multiseq with no structure
// data loaded at all.
vmd_msleep(1); // sleep for 1 millisecond or more
if (elapsed < 5 + 3) { // display the title screen, no animation
if (!letterson) {
letterson = TRUE;
redraw_list();
}
return;
}
elapsed -= 3;
if (letterson) {
letterson = FALSE;
redraw_list();
}
if (elapsed < 30) { // just spin the VMD logo
delta = elapsed - 5;
rot_on();
set_rot(solve_position((float) delta, 25.0f, 0.0f, 360.0f*8.0f), 'y');
rot_off();
}
if (elapsed < 15) {
delta = elapsed - 5;
scale_on();
set_scale( 1.0f/(1.0f+ ((float) delta)/3.0f)); // and getting smaller
scale_off();
glob_trans_on();
// and moving up
set_glob_trans(0, 0.5f, solve_position((float) delta, 10.0f, 0.0f, 0.5f));
glob_trans_off();
return;
}
if (elapsed < 20) {
return;
}
// I am at ( 0 , 0.5, 0.5)
// I want to get to ( -.7 , 0.9 , 0.5) in 10 secs
if (elapsed < 30) {
delta = elapsed - 20;
glob_trans_on();
set_glob_trans(
solve_position((float) delta, 10.0f, 0.0f, -0.6f * disp->aspect()),
solve_position((float) delta, 10.0f, 0.5f, 0.8f),
solve_position((float) delta, 10.0f, 0.5f, 0.5f));
glob_trans_off();
scale_on();
set_scale(solve_position((float) delta, 10.0f, 1.0f/(1.0f+10.0f/3.0f), 0.25f));
scale_off();
return;
}
if (elapsed < 35)
return;
// just spin the VMD logo
delta = elapsed - 35;
rot_on();
set_rot((float) delta * 360.0f / 6.0f, 'y');
rot_off();
}
time_type operator-=(const time_duration_type& td)
{
time_ = (time_system::get_time_rep(date(), time_of_day() - td));
return time_type(time_);
}
std::string terrama2::core::DataStoragerTiff::replaceMask(const std::string& mask,
std::shared_ptr<te::dt::DateTime> timestamp,
terrama2::core::DataSetPtr dataSet) const
{
if(!timestamp.get())
return mask;
long year = 0;
long month = 0;
long day = 0;
long hour = 0;
long minutes = 0;
long seconds = 0;
if(timestamp->getDateTimeType() == te::dt::TIME_INSTANT)
{
auto dateTime = std::dynamic_pointer_cast<te::dt::TimeInstant>(timestamp);
//invalid date type
if(dateTime->getTimeInstant().is_not_a_date_time())
return mask;
auto date = dateTime->getDate();
year = date.getYear();
month = date.getMonth().as_number();
day = date.getDay().as_number();
auto time = dateTime->getTime();
hour = time.getHours();
minutes = time.getMinutes();
seconds = time.getSeconds();
}
else if(timestamp->getDateTimeType() == te::dt::TIME_INSTANT_TZ)
{
auto dateTime = std::dynamic_pointer_cast<te::dt::TimeInstantTZ>(timestamp);
auto boostLocalTime = dateTime->getTimeInstantTZ();
//invalid date type
if(boostLocalTime.is_not_a_date_time())
return mask;
std::string timezone;
try
{
//get dataset timezone
timezone = getTimezone(dataSet);
}
catch(const terrama2::core::UndefinedTagException&)
{
//if no timezone is set use UTC
timezone = "UTC+00";
}
boost::local_time::time_zone_ptr zone(new boost::local_time::posix_time_zone(timezone));
auto localTime = boostLocalTime.local_time_in(zone);
auto date = localTime.date();
year = date.year();
month = date.month().as_number();
day = date.day();
auto time = localTime.time_of_day();
hour = time.hours();
minutes = time.minutes();
seconds = time.seconds();
}
else
{
//This method expects a valid Date/Time, other formats are not valid.
QString errMsg = QObject::tr("Unknown date format.");
TERRAMA2_LOG_ERROR() << errMsg;
throw terrama2::core::DataAccessorException() << ErrorDescription(errMsg);
}
//replace wildcards in mask
std::string fileName = mask;
size_t pos = fileName.find("yyyy");
if(pos != std::string::npos)
fileName.replace(pos, 4, zeroPadNumber(year, 4));
pos = fileName.find("yy");
if(pos != std::string::npos)
fileName.replace(pos, 2, zeroPadNumber(year, 2));
pos = fileName.find("MM");
if(pos != std::string::npos)
fileName.replace(pos, 2, zeroPadNumber(month, 2));
pos = fileName.find("dd");
if(pos != std::string::npos)
fileName.replace(pos, 2, zeroPadNumber(day, 2));
pos = fileName.find("hh");
if(pos != std::string::npos)
fileName.replace(pos, 2, zeroPadNumber(hour, 2));
pos = fileName.find("mm");
if(pos != std::string::npos)
fileName.replace(pos, 2, zeroPadNumber(minutes, 2));
pos = fileName.find("ss");
if(pos != std::string::npos)
fileName.replace(pos, 2, zeroPadNumber(seconds, 2));
//if no extension in the mask, add extension
pos = fileName.find(".tif");
if(pos != std::string::npos)
fileName += ".tif";
return fileName;
}