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

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12650 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2014-10-28 19:53:17 +00:00
parent 7cea65198f
commit 51a148df16
18 changed files with 632 additions and 274 deletions
Download Patch File Download Diff File Expand all files Collapse all files

132
lib/colvars/colvar.cpp
View File

@ -53,11 +53,17 @@ colvar::colvar (std::string const &conf)
if (cvcp != NULL) { \
cvcs.push_back (cvcp); \
cvcp->check_keywords (def_conf, def_config_key); \
if (cvm::get_error()) { \
cvm::error("Error: in setting up component \"" \
def_config_key"\".\n"); \
return; \
} \
cvm::decrease_depth(); \
} else { \
cvm::error ("Error: in allocating component \"" \
cvm::error("Error: in allocating component \"" \
def_config_key"\".\n", \
MEMORY_ERROR); \
return; \
} \
if ( (cvcp->period != 0.0) || (cvcp->wrap_center != 0.0) ) { \
if ( (cvcp->function_type != std::string ("distance_z")) && \
@ -70,6 +76,7 @@ colvar::colvar (std::string const &conf)
"Period: "+cvm::to_str(cvcp->period) + \
" wrapAround: "+cvm::to_str(cvcp->wrap_center), \
INPUT_ERROR); \
return; \
} \
} \
if ( ! cvcs.back()->name.size()) \
@ -150,63 +157,64 @@ colvar::colvar (std::string const &conf)
"", colvarparse::parse_silent)) {
enable(task_scripted);
cvm::log("This colvar is a scripted function.");
cvm::log("This colvar uses scripted function \"" + scripted_function + "\".");
std::string type_str;
get_keyval (conf, "scriptedFunctionType", type_str, "scalar");
// 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.type());
x.type(colvarvalue::type_notset);
for (i = 0; i < colvarvalue::type_all; i++) {
if (type_str == colvarvalue::type_keyword[i]) {
x.type(colvarvalue::Type(i));
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()]);
// Build ordered list of component values that will be
// passed to the script
// Sort array of cvcs based on values of componentExp
std::vector<cvc *> temp_vec;
for (i = 1; i <= cvcs.size(); i++) {
for (j = 0; j < cvcs.size(); j++) {
if (cvcs[j]->sup_np == int(i)) {
sorted_cvc_values.push_back(cvcs[j]->p_value());
temp_vec.push_back(cvcs[j]);
break;
}
}
}
if (sorted_cvc_values.size() != cvcs.size()) {
cvm::error("Could not find order numbers for all components"
if (temp_vec.size() != cvcs.size()) {
cvm::error("Could not find order numbers for all components "
"in componentExp values.");
return;
}
cvcs = temp_vec;
// Build ordered list of component values that will be
// passed to the script
for (j = 0; j < cvcs.size(); j++) {
sorted_cvc_values.push_back(cvcs[j]->p_value());
}
}
// this is set false if any of the components has an exponent
// different from 1 in the polynomial
b_linear = true;
// these will be set to false if any of the cvcs has them false
b_inverse_gradients = true;
b_Jacobian_force = true;
if (!tasks[task_scripted]) {
// this is set false if any of the components has an exponent
// different from 1 in the polynomial
b_linear = true;
// these will be set to false if any of the cvcs has them false
b_inverse_gradients = true;
b_Jacobian_force = true;
}
// Test whether this is a single-component variable
// Decide whether the colvar is periodic
// Used to wrap extended DOF if extendedLagrangian is on
if (cvcs.size() == 1 && (cvcs[0])->b_periodic && (cvcs[0])->sup_np == 1
&& (cvcs[0])->sup_coeff == 1.0 ) {
this->b_periodic = true;
this->period = (cvcs[0])->period;
if (cvcs.size() == 1 && (cvcs[0])->sup_np == 1
&& (cvcs[0])->sup_coeff == 1.0
&& !tasks[task_scripted]) {
b_single_cvc = true;
b_periodic = (cvcs[0])->b_periodic;
period = (cvcs[0])->period;
// TODO write explicit wrap() function for colvars to allow for
// sup_coeff different from 1
// this->period = (cvcs[0])->period * (cvcs[0])->sup_coeff;
} else {
this->b_periodic = false;
this->period = 0.0;
b_single_cvc = false;
b_periodic = false;
period = 0.0;
}
// check the available features of each cvc
@ -808,13 +816,14 @@ void colvar::calc()
// each atom group will take care of its own ref_pos_group, if defined
}
}
if (tasks[task_output_velocity]) {
for (i = 0; i < cvcs.size(); i++) {
for (ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
cvcs[i]->atom_groups[ig]->read_velocities();
}
}
}
//// Don't try to get atom velocities, as no back-end currently implements it
// if (tasks[task_output_velocity] && !tasks[task_fdiff_velocity]) {
// for (i = 0; i < cvcs.size(); i++) {
// for (ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
// cvcs[i]->atom_groups[ig]->read_velocities();
// }
// }
// }
if (tasks[task_system_force]) {
for (i = 0; i < cvcs.size(); i++) {
for (ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
@ -1153,8 +1162,11 @@ void colvar::communicate_forces()
for (i = 0; i < cvcs.size(); i++) {
cvm::increase_depth();
// Note: we need a dot product here
(cvcs[i])->apply_force (f * func_grads[i]);
// 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]);
cvm::decrease_depth();
}
} else if (x.type() == colvarvalue::type_scalar) {
@ -1223,30 +1235,38 @@ bool colvar::periodic_boundaries() const
cvm::real colvar::dist2 (colvarvalue const &x1,
colvarvalue const &x2) const
{
return (cvcs[0])->dist2 (x1, x2);
if (b_single_cvc) {
return (cvcs[0])->dist2(x1, x2);
} else {
return x1.dist2(x2);
}
}
colvarvalue colvar::dist2_lgrad (colvarvalue const &x1,
colvarvalue const &x2) const
{
return (cvcs[0])->dist2_lgrad (x1, x2);
if (b_single_cvc) {
return (cvcs[0])->dist2_lgrad (x1, x2);
} else {
return x1.dist2_grad(x2);
}
}
colvarvalue colvar::dist2_rgrad (colvarvalue const &x1,
colvarvalue const &x2) const
{
return (cvcs[0])->dist2_rgrad (x1, x2);
}
cvm::real colvar::compare (colvarvalue const &x1,
colvarvalue const &x2) const
{
return (cvcs[0])->compare (x1, x2);
if (b_single_cvc) {
return (cvcs[0])->dist2_rgrad (x1, x2);
} else {
return x2.dist2_grad(x1);
}
}
void colvar::wrap (colvarvalue &x) const
{
(cvcs[0])->wrap (x);
if (b_single_cvc) {
(cvcs[0])->wrap (x);
}
return;
}