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Update Colvars to version 2017-07-15 and support automated builds for it

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This commit is contained in:
Giacomo Fiorin
2017-07-19 14:10:43 -04:00
parent cc9b3864bf
commit ee6cac826e
52 changed files with 3473 additions and 2413 deletions
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178
lib/colvars/colvarmodule.cpp
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@ -21,10 +21,14 @@
#include "colvarbias_meta.h"
#include "colvarbias_restraint.h"
#include "colvarscript.h"
#include "colvaratoms.h"
colvarmodule::colvarmodule(colvarproxy *proxy_in)
{
depth_s = 0;
cv_traj_os = NULL;
// pointer to the proxy object
if (proxy == NULL) {
proxy = proxy_in;
@ -33,12 +37,10 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in)
// TODO relax this error to handle multiple molecules in VMD
// once the module is not static anymore
cvm::error("Error: trying to allocate the collective "
"variable module twice.\n");
"variable module twice.\n", BUG_ERROR);
return;
}
depth_s = 0;
cvm::log(cvm::line_marker);
cvm::log("Initializing the collective variables module, version "+
cvm::to_str(COLVARS_VERSION)+".\n");
@ -222,9 +224,9 @@ int colvarmodule::parse_config(std::string &conf)
// update any necessary proxy data
proxy->setup();
if (cv_traj_os.is_open()) {
if (cv_traj_os != NULL) {
// configuration might have changed, better redo the labels
write_traj_label(cv_traj_os);
write_traj_label(*cv_traj_os);
}
return get_error();
@ -295,7 +297,7 @@ int colvarmodule::parse_colvars(std::string const &conf)
std::string colvar_conf = "";
size_t pos = 0;
while (parse->key_lookup(conf, "colvar", colvar_conf, pos)) {
while (parse->key_lookup(conf, "colvar", &colvar_conf, &pos)) {
if (colvar_conf.size()) {
cvm::log(cvm::line_marker);
@ -350,7 +352,7 @@ int colvarmodule::parse_biases_type(std::string const &conf,
{
std::string bias_conf = "";
size_t conf_saved_pos = 0;
while (parse->key_lookup(conf, keyword, bias_conf, conf_saved_pos)) {
while (parse->key_lookup(conf, keyword, &bias_conf, &conf_saved_pos)) {
if (bias_conf.size()) {
cvm::log(cvm::line_marker);
cvm::increase_depth();
@ -409,12 +411,6 @@ int colvarmodule::parse_biases(std::string const &conf)
size_t i;
for (i = 0; i < biases.size(); i++) {
biases[i]->enable(colvardeps::f_cvb_active);
if (cvm::debug())
biases[i]->print_state();
}
size_t n_hist_dep_biases = 0;
std::vector<std::string> hist_dep_biases_names;
for (i = 0; i < biases.size(); i++) {
@ -487,7 +483,8 @@ int colvarmodule::catch_input_errors(int result)
}
colvarbias * colvarmodule::bias_by_name(std::string const &name) {
colvarbias * colvarmodule::bias_by_name(std::string const &name)
{
colvarmodule *cv = cvm::main();
for (std::vector<colvarbias *>::iterator bi = cv->biases.begin();
bi != cv->biases.end();
@ -500,7 +497,8 @@ colvarbias * colvarmodule::bias_by_name(std::string const &name) {
}
colvar *colvarmodule::colvar_by_name(std::string const &name) {
colvar *colvarmodule::colvar_by_name(std::string const &name)
{
colvarmodule *cv = cvm::main();
for (std::vector<colvar *>::iterator cvi = cv->colvars.begin();
cvi != cv->colvars.end();
@ -513,6 +511,20 @@ colvar *colvarmodule::colvar_by_name(std::string const &name) {
}
cvm::atom_group *colvarmodule::atom_group_by_name(std::string const &name)
{
colvarmodule *cv = cvm::main();
for (std::vector<cvm::atom_group *>::iterator agi = cv->named_atom_groups.begin();
agi != cv->named_atom_groups.end();
agi++) {
if ((*agi)->name == name) {
return (*agi);
}
}
return NULL;
}
int colvarmodule::change_configuration(std::string const &bias_name,
std::string const &conf)
{
@ -521,7 +533,10 @@ int colvarmodule::change_configuration(std::string const &bias_name,
cvm::increase_depth();
colvarbias *b;
b = bias_by_name(bias_name);
if (b == NULL) { cvm::error("Error: bias not found: " + bias_name); }
if (b == NULL) {
cvm::error("Error: bias not found: " + bias_name);
return COLVARS_ERROR;
}
b->change_configuration(conf);
cvm::decrease_depth();
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
@ -534,7 +549,10 @@ std::string colvarmodule::read_colvar(std::string const &name)
colvar *c;
std::stringstream ss;
c = colvar_by_name(name);
if (c == NULL) { cvm::fatal_error("Error: colvar not found: " + name); }
if (c == NULL) {
cvm::error("Error: colvar not found: " + name);
return std::string();
}
ss << c->value();
cvm::decrease_depth();
return ss.str();
@ -547,7 +565,10 @@ cvm::real colvarmodule::energy_difference(std::string const &bias_name,
colvarbias *b;
cvm::real energy_diff = 0.;
b = bias_by_name(bias_name);
if (b == NULL) { cvm::fatal_error("Error: bias not found: " + bias_name); }
if (b == NULL) {
cvm::error("Error: bias not found: " + bias_name);
return 0.;
}
energy_diff = b->energy_difference(conf);
cvm::decrease_depth();
return energy_diff;
@ -666,18 +687,36 @@ int colvarmodule::calc_colvars()
cvm::log("Calculating collective variables.\n");
// calculate collective variables and their gradients
// First, we need to decide which biases are awake
// so they can activate colvars as needed
std::vector<colvarbias *>::iterator bi;
for (bi = biases.begin(); bi != biases.end(); bi++) {
int tsf = (*bi)->get_time_step_factor();
if (tsf > 0 && (step_absolute() % tsf == 0)) {
(*bi)->enable(colvardeps::f_cvb_awake);
} else {
(*bi)->disable(colvardeps::f_cvb_awake);
}
}
int error_code = COLVARS_OK;
std::vector<colvar *>::iterator cvi;
// Determine which colvars are active at this iteration
variables_active()->resize(0);
variables_active()->clear();
variables_active()->reserve(variables()->size());
for (cvi = variables()->begin(); cvi != variables()->end(); cvi++) {
// This is a dynamic feature - the next call should be to enable()
// or disable() when dynamic dependency resolution is fully implemented
(*cvi)->set_enabled(colvardeps::f_cv_active,
step_absolute() % (*cvi)->get_time_step_factor() == 0);
variables_active()->push_back(*cvi);
// Wake up or put to sleep variables
int tsf = (*cvi)->get_time_step_factor();
if (tsf > 0 && (step_absolute() % tsf == 0)) {
(*cvi)->enable(colvardeps::f_cv_awake);
} else {
(*cvi)->disable(colvardeps::f_cv_awake);
}
if ((*cvi)->is_enabled()) {
variables_active()->push_back(*cvi);
}
}
// if SMP support is available, split up the work
@ -685,8 +724,8 @@ int colvarmodule::calc_colvars()
// first, calculate how much work (currently, how many active CVCs) each colvar has
variables_active_smp()->resize(0);
variables_active_smp_items()->resize(0);
variables_active_smp()->clear();
variables_active_smp_items()->clear();
variables_active_smp()->reserve(variables_active()->size());
variables_active_smp_items()->reserve(variables_active()->size());
@ -748,7 +787,8 @@ int colvarmodule::calc_biases()
total_bias_energy = 0.0;
// update the list of active biases
biases_active()->resize(0);
// which may have changed based on f_cvb_awake in calc_colvars()
biases_active()->clear();
biases_active()->reserve(biases.size());
for (bi = biases.begin(); bi != biases.end(); bi++) {
if ((*bi)->is_enabled()) {
@ -828,8 +868,7 @@ int colvarmodule::update_colvar_forces()
"of colvars (if they have any).\n");
cvm::increase_depth();
for (cvi = variables()->begin(); cvi != variables()->end(); cvi++) {
// Here we call even inactive colvars, so they accumulate biasing forces
// as well as update their extended-system dynamics
// Inactive colvars will only reset their forces and return 0 energy
total_colvar_energy += (*cvi)->update_forces_energy();
if (cvm::get_error()) {
return COLVARS_ERROR;
@ -883,11 +922,13 @@ int colvarmodule::write_restart_files()
((cvm::step_absolute() % restart_out_freq) == 0) ) {
cvm::log("Writing the state file \""+
restart_out_name+"\".\n");
proxy->backup_file(restart_out_name.c_str());
restart_out_os.open(restart_out_name.c_str());
if (!restart_out_os.is_open() || !write_restart(restart_out_os))
cvm::error("Error: in writing restart file.\n");
restart_out_os.close();
proxy->backup_file(restart_out_name);
std::ostream *restart_out_os = proxy->output_stream(restart_out_name);
if (!restart_out_os) return cvm::get_error();
if (!write_restart(*restart_out_os)) {
return cvm::error("Error: in writing restart file.\n", FILE_ERROR);
}
proxy->close_output_stream(restart_out_name);
}
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
@ -896,26 +937,26 @@ int colvarmodule::write_restart_files()
int colvarmodule::write_traj_files()
{
if (!cv_traj_os.is_open()) {
if (cv_traj_os == NULL) {
open_traj_file(cv_traj_name);
}
// write labels in the traj file every 1000 lines and at first timestep
if ((cvm::step_absolute() % (cv_traj_freq * 1000)) == 0 || cvm::step_relative() == 0) {
write_traj_label(cv_traj_os);
write_traj_label(*cv_traj_os);
}
if ((cvm::step_absolute() % cv_traj_freq) == 0) {
write_traj(cv_traj_os);
write_traj(*cv_traj_os);
}
if (restart_out_freq && cv_traj_os.is_open()) {
if (restart_out_freq && (cv_traj_os != NULL)) {
// flush the trajectory file if we are at the restart frequency
if ( (cvm::step_relative() > 0) &&
((cvm::step_absolute() % restart_out_freq) == 0) ) {
cvm::log("Synchronizing (emptying the buffer of) trajectory file \""+
cv_traj_name+"\".\n");
cv_traj_os.flush();
proxy->flush_output_stream(cv_traj_os);
}
}
@ -1003,9 +1044,11 @@ int colvarmodule::reset()
index_groups.clear();
index_group_names.clear();
if (cv_traj_os.is_open()) {
proxy->reset();
if (cv_traj_os != NULL) {
// Do not close file here, as we might not be done with it yet.
cv_traj_os.flush();
proxy->flush_output_stream(cv_traj_os);
}
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
@ -1264,9 +1307,9 @@ int colvarmodule::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();
if (cv_traj_os != NULL) {
// do not close, there may be another run command
proxy->flush_output_stream(cv_traj_os);
}
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
@ -1380,9 +1423,10 @@ std::ostream & colvarmodule::write_restart(std::ostream &os)
return os;
}
int colvarmodule::open_traj_file(std::string const &file_name)
{
if (cv_traj_os.is_open()) {
if (cv_traj_os != NULL) {
return COLVARS_OK;
}
@ -1390,36 +1434,35 @@ int colvarmodule::open_traj_file(std::string const &file_name)
if (cv_traj_append) {
cvm::log("Appending to colvar trajectory file \""+file_name+
"\".\n");
cv_traj_os.open(file_name.c_str(), std::ios::app);
cv_traj_os = (cvm::proxy)->output_stream(file_name, std::ios::app);
} else {
cvm::log("Writing to colvar trajectory file \""+file_name+
"\".\n");
proxy->backup_file(file_name.c_str());
cv_traj_os.open(file_name.c_str());
cv_traj_os = (cvm::proxy)->output_stream(file_name);
}
if (!cv_traj_os.is_open()) {
if (cv_traj_os == NULL) {
cvm::error("Error: cannot write to file \""+file_name+"\".\n",
FILE_ERROR);
}
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
return cvm::get_error();
}
int colvarmodule::close_traj_file()
{
if (cv_traj_os.is_open()) {
cv_traj_os.close();
if (cv_traj_os != NULL) {
proxy->close_output_stream(cv_traj_name);
cv_traj_os = NULL;
}
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
return cvm::get_error();
}
std::ostream & colvarmodule::write_traj_label(std::ostream &os)
{
if (!os.good()) {
cvm::error("Cannot write to trajectory file.");
return os;
}
os.setf(std::ios::scientific, std::ios::floatfield);
os << "# " << cvm::wrap_string("step", cvm::it_width-2)
@ -1437,13 +1480,16 @@ std::ostream & colvarmodule::write_traj_label(std::ostream &os)
(*bi)->write_traj_label(os);
}
os << "\n";
if (cvm::debug()) {
os.flush();
proxy->flush_output_stream(&os);
}
cvm::decrease_depth();
return os;
}
std::ostream & colvarmodule::write_traj(std::ostream &os)
{
os.setf(std::ios::scientific, std::ios::floatfield);
@ -1463,9 +1509,11 @@ std::ostream & colvarmodule::write_traj(std::ostream &os)
(*bi)->write_traj(os);
}
os << "\n";
if (cvm::debug()) {
os.flush();
proxy->flush_output_stream(&os);
}
cvm::decrease_depth();
return os;
}
@ -1540,25 +1588,19 @@ void colvarmodule::clear_error()
}
void cvm::error(std::string const &message, int code)
int colvarmodule::error(std::string const &message, int code)
{
set_error_bits(code);
proxy->error(message);
return get_error();
}
void cvm::fatal_error(std::string const &message)
int colvarmodule::fatal_error(std::string const &message)
{
// TODO once all non-fatal errors have been set to be handled by error(),
// set DELETE_COLVARS here for VMD to handle it
set_error_bits(FATAL_ERROR);
proxy->fatal_error(message);
}
void cvm::exit(std::string const &message)
{
proxy->exit(message);
return get_error();
}