ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Update Colvars module to version 2017-03-10

Browse Source
This commit is contained in:
Giacomo Fiorin
2017-03-10 09:16:58 -05:00
parent 79b005dc3d
commit 5fe6206638
29 changed files with 1371 additions and 868 deletions
Download Patch File Download Diff File Expand all files Collapse all files

51
lib/colvars/colvarbias.cpp
View File

@ -19,20 +19,6 @@ colvarbias::colvarbias(char const *key)
rank = 1;
if (bias_type == std::string("abf")) {
rank = cvm::n_abf_biases+1;
}
if (bias_type == std::string("harmonic") ||
bias_type == std::string("linear")) {
rank = cvm::n_rest_biases+1;
}
if (bias_type == std::string("histogram")) {
rank = cvm::n_histo_biases+1;
}
if (bias_type == std::string("metadynamics")) {
rank = cvm::n_meta_biases+1;
}
has_data = false;
b_output_energy = false;
reset();
@ -48,7 +34,11 @@ int colvarbias::init(std::string const &conf)
colvarparse::init(conf);
if (name.size() == 0) {
// first initialization
cvm::log("Initializing a new \""+bias_type+"\" instance.\n");
rank = cvm::num_biases_type(bias_type);
get_keyval(conf, "name", name, bias_type+cvm::to_str(rank));
{
@ -69,7 +59,7 @@ int colvarbias::init(std::string const &conf)
// lookup the associated colvars
std::vector<std::string> colvar_names;
if (get_keyval(conf, "colvars", colvar_names)) {
if (colvars.size()) {
if (num_variables()) {
cvm::error("Error: cannot redefine the colvars that a bias was already defined on.\n",
INPUT_ERROR);
return INPUT_ERROR;
@ -80,7 +70,7 @@ int colvarbias::init(std::string const &conf)
}
}
if (!colvars.size()) {
if (!num_variables()) {
cvm::error("Error: no collective variables specified.\n", INPUT_ERROR);
return INPUT_ERROR;
}
@ -89,6 +79,8 @@ int colvarbias::init(std::string const &conf)
cvm::log("Reinitializing bias \""+name+"\".\n");
}
output_prefix = cvm::output_prefix();
get_keyval(conf, "outputEnergy", b_output_energy, b_output_energy);
return COLVARS_OK;
@ -98,7 +90,7 @@ int colvarbias::init(std::string const &conf)
int colvarbias::reset()
{
bias_energy = 0.0;
for (size_t i = 0; i < colvars.size(); i++) {
for (size_t i = 0; i < num_variables(); i++) {
colvar_forces[i].reset();
}
return COLVARS_OK;
@ -132,12 +124,13 @@ int colvarbias::clear()
}
}
colvarmodule *cv = cvm::main();
// ...and from the colvars module
for (std::vector<colvarbias *>::iterator bi = cvm::biases.begin();
bi != cvm::biases.end();
for (std::vector<colvarbias *>::iterator bi = cv->biases.begin();
bi != cv->biases.end();
++bi) {
if ( *bi == this) {
cvm::biases.erase(bi);
cv->biases.erase(bi);
break;
}
}
@ -185,21 +178,29 @@ int colvarbias::add_colvar(std::string const &cv_name)
int colvarbias::update()
{
// Note: if anything is added here, it should be added also in the SMP block of calc_biases()
// TODO move here debug msg of bias update
if (cvm::debug()) {
cvm::log("Updating the "+bias_type+" bias \""+this->name+"\".\n");
}
has_data = true;
bias_energy = 0.0;
for (size_t ir = 0; ir < num_variables(); ir++) {
colvar_forces[ir].reset();
}
return COLVARS_OK;
}
void colvarbias::communicate_forces()
{
for (size_t i = 0; i < colvars.size(); i++) {
for (size_t i = 0; i < num_variables(); i++) {
if (cvm::debug()) {
cvm::log("Communicating a force to colvar \""+
colvars[i]->name+"\".\n");
variables(i)->name+"\".\n");
}
colvars[i]->add_bias_force(colvar_forces[i]);
variables(i)->add_bias_force(colvar_forces[i]);
}
}