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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13444 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2015-04-30 14:09:42 +00:00
parent 71df48bd6a
commit f539e43b22
22 changed files with 438 additions and 625 deletions
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45
lib/colvars/colvarmodule.cpp
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@ -8,9 +8,10 @@
#include "colvarproxy.h"
#include "colvar.h"
#include "colvarbias.h"
#include "colvarbias_alb.h"
#include "colvarbias_meta.h"
#include "colvarbias_abf.h"
#include "colvarbias_alb.h"
#include "colvarbias_histogram.h"
#include "colvarbias_meta.h"
#include "colvarbias_restraint.h"
#include "colvarscript.h"
@ -523,13 +524,13 @@ int colvarmodule::calc() {
cvm::log("Perform runtime analyses.\n");
cvm::increase_depth();
for (cvi = colvars.begin(); cvi != colvars.end(); cvi++) {
(*cvi)->analyse();
(*cvi)->analyze();
if (cvm::get_error()) {
return COLVARS_ERROR;
}
}
for (bi = biases.begin(); bi != biases.end(); bi++) {
(*bi)->analyse();
(*bi)->analyze();
if (cvm::get_error()) {
return COLVARS_ERROR;
}
@ -627,7 +628,7 @@ int colvarmodule::analyze()
cvi != colvars.end();
cvi++) {
cvm::increase_depth();
(*cvi)->analyse();
(*cvi)->analyze();
cvm::decrease_depth();
}
@ -636,7 +637,7 @@ int colvarmodule::analyze()
bi != biases.end();
bi++) {
cvm::increase_depth();
(*bi)->analyse();
(*bi)->analyze();
cvm::decrease_depth();
}
@ -717,13 +718,15 @@ int colvarmodule::setup_input()
cvm::log(cvm::line_marker);
}
}
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}
int colvarmodule::setup_output()
{
int error_code = 0;
// output state file (restart)
restart_out_name = proxy->restart_output_prefix().size() ?
std::string(proxy->restart_output_prefix()+".colvars.state") :
@ -748,7 +751,17 @@ int colvarmodule::setup_output()
std::string(""));
if (cv_traj_freq && cv_traj_name.size()) {
open_traj_file(cv_traj_name);
error_code |= open_traj_file(cv_traj_name);
}
for (std::vector<colvarbias *>::iterator bi = biases.begin();
bi != biases.end();
bi++) {
error_code |= (*bi)->setup_output();
}
if (error_code != COLVARS_OK || cvm::get_error()) {
set_error_bits(FILE_ERROR);
}
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
@ -828,6 +841,14 @@ int colvarmodule::write_output_files()
}
cvm::decrease_depth();
cvm::increase_depth();
for (std::vector<colvarbias *>::iterator bi = biases.begin();
bi != biases.end();
bi++) {
(*bi)->write_output_files();
}
cvm::decrease_depth();
if (cv_traj_os.is_open()) {
// do not close to avoid problems with multiple NAMD runs
cv_traj_os.flush();
@ -839,8 +860,8 @@ int colvarmodule::write_output_files()
int colvarmodule::read_traj(char const *traj_filename,
size_t traj_read_begin,
size_t traj_read_end)
long traj_read_begin,
long traj_read_end)
{
cvm::log("Opening trajectory file \""+
std::string(traj_filename)+"\".\n");
@ -1204,8 +1225,8 @@ colvarproxy *colvarmodule::proxy = NULL;
// static runtime data
cvm::real colvarmodule::debug_gradients_step_size = 1.0e-03;
int colvarmodule::errorCode = 0;
size_t colvarmodule::it = 0;
size_t colvarmodule::it_restart = 0;
long colvarmodule::it = 0;
long colvarmodule::it_restart = 0;
size_t colvarmodule::restart_out_freq = 0;
size_t colvarmodule::cv_traj_freq = 0;
size_t colvarmodule::depth = 0;