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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14829 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2016-04-15 16:07:01 +00:00
parent 32509da721
commit 212a955285
31 changed files with 1713 additions and 1493 deletions
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23
lib/colvars/colvarbias.cpp
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@ -10,6 +10,8 @@ colvarbias::colvarbias(std::string const &conf, char const *key)
{
cvm::log("Initializing a new \""+std::string(key)+"\" instance.\n");
init_cvb_requires();
size_t rank = 1;
std::string const key_str(key);
@ -35,6 +37,8 @@ colvarbias::colvarbias(std::string const &conf, char const *key)
return;
}
description = "bias " + name;
// lookup the associated colvars
std::vector<std::string> colvars_str;
if (get_keyval(conf, "colvars", colvars_str)) {
@ -46,6 +50,13 @@ colvarbias::colvarbias(std::string const &conf, char const *key)
cvm::error("Error: no collective variables specified.\n");
return;
}
for (size_t i=0; i<colvars.size(); i++) {
// All biases need at least the value of colvars
// although possibly not at all timesteps
add_child(colvars[i]);
}
// Start in active state by default
enable(f_cvb_active);
get_keyval(conf, "outputEnergy", b_output_energy, false);
}
@ -84,7 +95,8 @@ colvarbias::~colvarbias()
void colvarbias::add_colvar(std::string const &cv_name)
{
if (colvar *cv = cvm::colvar_by_name(cv_name)) {
cv->enable(colvar::task_gradients);
// Removed this as nor all biases apply forces eg histogram
// cv->enable(colvar::task_gradients);
if (cvm::debug())
cvm::log("Applying this bias to collective variable \""+
cv->name+"\".\n");
@ -100,10 +112,11 @@ void colvarbias::add_colvar(std::string const &cv_name)
}
cvm::real colvarbias::update()
int colvarbias::update()
{
// Note: if anything is added here, it should be added also in the SMP block of calc_biases()
has_data = true;
return 0.0;
return COLVARS_OK;
}
@ -172,3 +185,7 @@ std::ostream & colvarbias::write_traj(std::ostream &os)
<< bias_energy;
return os;
}
// Static members
std::vector<cvm::deps::feature *> colvarbias::cvb_features;