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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15315 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2016-07-15 22:25:17 +00:00
parent d32f1ea4c0
commit 05398a6863
19 changed files with 420 additions and 178 deletions
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35
lib/colvars/colvarbias_abf.cpp
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@ -4,16 +4,24 @@
#include "colvar.h"
#include "colvarbias_abf.h"
/// ABF bias constructor; parses the config file
colvarbias_abf::colvarbias_abf(std::string const &conf, char const *key)
: colvarbias(conf, key),
colvarbias_abf::colvarbias_abf(char const *key)
: colvarbias(key),
force(NULL),
gradients(NULL),
samples(NULL),
last_gradients(NULL),
last_samples(NULL)
{
}
int colvarbias_abf::init(std::string const &conf)
{
colvarbias::init(conf);
provide(f_cvb_history_dependent);
// TODO relax this in case of VMD plugin
if (cvm::temperature() == 0.0)
cvm::log("WARNING: ABF should not be run without a thermostat or at 0 Kelvin!\n");
@ -21,10 +29,18 @@ colvarbias_abf::colvarbias_abf(std::string const &conf, char const *key)
// ************* parsing general ABF options ***********************
get_keyval(conf, "applyBias", apply_bias, true);
if (!apply_bias) cvm::log("WARNING: ABF biases will *not* be applied!\n");
if (apply_bias) {
enable(f_cvb_apply_force);
} else {
cvm::log("WARNING: ABF biases will *not* be applied!\n");
}
get_keyval(conf, "updateBias", update_bias, true);
if (!update_bias) cvm::log("WARNING: ABF biases will *not* be updated!\n");
if (update_bias) {
enable(f_cvb_history_dependent);
} else {
cvm::log("WARNING: ABF biases will *not* be updated!\n");
}
get_keyval(conf, "hideJacobian", hide_Jacobian, false);
if (hide_Jacobian) {
@ -38,7 +54,7 @@ colvarbias_abf::colvarbias_abf(std::string const &conf, char const *key)
min_samples = full_samples / 2;
// full_samples - min_samples >= 1 is guaranteed
get_keyval(conf, "inputPrefix", input_prefix, std::vector<std::string> ());
get_keyval(conf, "inputPrefix", input_prefix, std::vector<std::string>());
get_keyval(conf, "outputFreq", output_freq, cvm::restart_out_freq);
get_keyval(conf, "historyFreq", history_freq, 0);
b_history_files = (history_freq > 0);
@ -63,10 +79,10 @@ colvarbias_abf::colvarbias_abf(std::string const &conf, char const *key)
if (update_bias) {
// Request calculation of system force (which also checks for availability)
if(enable(f_cvb_get_system_force)) return;
if(enable(f_cvb_get_system_force)) return cvm::get_error();
}
if (apply_bias) {
if(enable(f_cvb_apply_force)) return;
if(enable(f_cvb_apply_force)) return cvm::get_error();
}
for (size_t i = 0; i < colvars.size(); i++) {
@ -126,6 +142,8 @@ colvarbias_abf::colvarbias_abf(std::string const &conf, char const *key)
}
cvm::log("Finished ABF setup.\n");
return COLVARS_OK;
}
/// Destructor
@ -277,6 +295,7 @@ int colvarbias_abf::update()
return COLVARS_OK;
}
int colvarbias_abf::replica_share() {
int p;