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Update Colvars library to version 2019-04-26

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The following is list of relevant issues fixed and improvements:

Fix forces and missing output of runtime histogram for histogramRestraint
https://github.com/Colvars/colvars/pull/246

Use fix_modify to add configuration to Colvars:
https://github.com/Colvars/colvars/pull/216

Fix componentCoeff and name not working with orientationAngle components:
https://github.com/Colvars/colvars/issues/213

Fix 1-timestep offset with extendedLagrangian:
https://github.com/Colvars/colvars/pull/210

Changes to improve compiler support:
https://github.com/Colvars/colvars/pull/203

Fix ignored anisotropic cutoff3 for groupCoordNum:
https://github.com/Colvars/colvars/pull/202

New dipoleMagnitude variable:
https://github.com/Colvars/colvars/pull/198

Parser improvements:
https://github.com/Colvars/colvars/pull/196
This commit is contained in:
Giacomo Fiorin
2019-04-30 09:50:12 -04:00
parent 0005ee3e93
commit 7e00acce53
45 changed files with 2378 additions and 1328 deletions
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53
lib/colvars/colvarscript.cpp
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@ -137,6 +137,10 @@ int colvarscript::run(int objc, unsigned char *const objv[])
if (cmd == "update") {
error_code |= proxy->update_input();
if (error_code) {
result += "Error updating the Colvars module.\n";
return error_code;
}
error_code |= colvars->calc();
error_code |= proxy->update_output();
if (error_code) {
@ -273,6 +277,10 @@ int colvarscript::run(int objc, unsigned char *const objv[])
int colvarscript::proc_colvar(colvar *cv, int objc, unsigned char *const objv[]) {
if (objc < 3) {
result = "Missing arguments";
return COLVARSCRIPT_ERROR;
}
std::string const subcmd(obj_to_str(objv[2]));
if (subcmd == "value") {
@ -323,6 +331,47 @@ int colvarscript::proc_colvar(colvar *cv, int objc, unsigned char *const objv[])
return COLVARS_OK;
}
if (subcmd == "getatomgroups") {
std::vector<std::vector<int> > lists = cv->get_atom_lists();
std::vector<std::vector<int> >::iterator li = lists.begin();
for ( ; li != lists.end(); ++li) {
result += "{";
std::vector<int>::iterator lj = (*li).begin();
for ( ; lj != (*li).end(); ++lj) {
result += cvm::to_str(*lj);
result += " ";
}
result += "} ";
}
return COLVARS_OK;
}
if (subcmd == "getatomids") {
std::vector<int>::iterator li = cv->atom_ids.begin();
for ( ; li != cv->atom_ids.end(); ++li) {
result += cvm::to_str(*li);
result += " ";
}
return COLVARS_OK;
}
if (subcmd == "getgradients") {
std::vector<cvm::rvector>::iterator li = cv->atomic_gradients.begin();
for ( ; li != cv->atomic_gradients.end(); ++li) {
result += "{";
int j;
for (j = 0; j < 3; ++j) {
result += cvm::to_str((*li)[j]);
result += " ";
}
result += "} ";
}
return COLVARS_OK;
}
if (subcmd == "getappliedforce") {
result = (cv->applied_force()).to_simple_string();
return COLVARS_OK;
@ -410,6 +459,10 @@ int colvarscript::proc_colvar(colvar *cv, int objc, unsigned char *const objv[])
int colvarscript::proc_bias(colvarbias *b, int objc, unsigned char *const objv[]) {
if (objc < 3) {
result = "Missing arguments";
return COLVARSCRIPT_ERROR;
}
std::string const subcmd(obj_to_str(objv[2]));
if (subcmd == "energy") {