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update the colvars module to the version 2014-11-13

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This commit is contained in:
Axel Kohlmeyer
2014-11-14 18:34:33 +01:00
parent d5628a3058
commit 8b4ce4d893
11 changed files with 143 additions and 77 deletions
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66
lib/colvars/colvar.cpp
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@ -161,11 +161,33 @@ colvar::colvar(std::string const &conf)
enable(task_scripted);
cvm::log("This colvar uses scripted function \"" + scripted_function + "\".");
// Only accept scalar scripted colvars
// might accept other types when the infrastructure is in place
// for derivatives of vectors wrt vectors
x.type(colvarvalue::type_scalar);
x_reported.type(x);
std::string type_str;
get_keyval(conf, "scriptedFunctionType", type_str, "scalar");
x.type(colvarvalue::type_notset);
int t;
for (t = 0; t < colvarvalue::type_all; t++) {
if (type_str == colvarvalue::type_keyword(colvarvalue::Type(t))) {
x.type(colvarvalue::Type(t));
break;
}
}
if (x.type() == colvarvalue::type_notset) {
cvm::error("Could not parse scripted colvar type.");
return;
}
x_reported.type (x.type());
cvm::log(std::string("Expecting colvar value of type ")
+ colvarvalue::type_desc(x.type()));
if (x.type() == colvarvalue::type_vector) {
int size;
if (!get_keyval(conf, "scriptedFunctionVectorSize", size)) {
cvm::error("Error: no size specified for vector scripted function.");
return;
}
x.vector1d_value.resize(size);
}
// Sort array of cvcs based on values of componentExp
std::vector<cvc *> temp_vec;
@ -190,15 +212,6 @@ colvar::colvar(std::string const &conf)
sorted_cvc_values.push_back(&(cvcs[j]->value()));
}
// // these two are the vector value and the Jacobian matrix of the scripted function, respectively
// x_cvc.type(type_vector);
// dx_cvc.type(type_matrix); // TODO: not implemented yet
// for (j = 0; j < cvcs.size(); j++) {
// x_cvc.add_elem(cvcs[j]->value());
// dx_cvc.add_elem(cvcs[j]->value());
// }
b_homogeneous = false;
// Scripted functions are deemed non-periodic
b_periodic = false;
@ -1176,25 +1189,28 @@ void colvar::communicate_forces()
cvm::log("Communicating forces from colvar \""+this->name+"\".\n");
if (tasks[task_scripted]) {
std::vector<colvarvalue> func_grads(cvcs.size());
std::vector<cvm::matrix2d<cvm::real> > func_grads;
for (i = 0; i < cvcs.size(); i++) {
func_grads.push_back(cvm::matrix2d<cvm::real> (x.size(),
cvcs[i]->value().size()));
}
int res = cvm::proxy->run_colvar_gradient_callback(scripted_function, sorted_cvc_values, func_grads);
if (res == COLVARS_NOT_IMPLEMENTED) {
cvm::error("Colvar gradient scripts are not implemented.");
return;
}
if (res != COLVARS_OK) {
cvm::error("Error running colvar gradient script");
if (res == COLVARS_NOT_IMPLEMENTED) {
cvm::error("Colvar gradient scripts are not implemented.");
} else {
cvm::error("Error running colvar gradient script");
}
return;
}
for (i = 0; i < cvcs.size(); i++) {
cvm::increase_depth();
// Force is scalar times colvarvalue (scalar or vector)
// Note: this can only handle scalar colvars (scalar values of f)
// A non-scalar colvar would need the gradient to be expressed
// as an order-2 tensor
(cvcs[i])->apply_force(f.real_value * func_grads[i]);
// cvc force is colvar force times colvar/cvc Jacobian
// (vector-matrix product)
(cvcs[i])->apply_force(colvarvalue(f.as_vector() * func_grads[i],
cvcs[i]->value().type()));
cvm::decrease_depth();
}
} else if (x.type() == colvarvalue::type_scalar) {