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colvars update 2015-08-12

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This commit is contained in:
Axel Kohlmeyer
2015-08-14 09:28:24 -04:00
parent 0982c06bf5
commit 55c32a2e06
5 changed files with 50 additions and 102 deletions
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31
lib/colvars/colvar.cpp
View File

@ -846,7 +846,22 @@ void colvar::calc()
if (cvm::debug())
cvm::log("Collecting data from atom groups.\n");
// Update the enabled/disabled status of cvcs if necessary
if (cvc_flags.size()) {
bool any = false;
for (i = 0; i < cvcs.size(); i++) {
cvcs[i]->b_enabled = cvc_flags[i];
any = any || cvc_flags[i];
}
if (!any) {
cvm::error("ERROR: All CVCs are disabled for colvar " + this->name +"\n");
return;
}
cvc_flags.resize(0);
}
for (i = 0; i < cvcs.size(); i++) {
if (!cvcs[i]->b_enabled) continue;
for (ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
cvm::atom_group &atoms = *(cvcs[i]->atom_groups[ig]);
atoms.reset_atoms_data();
@ -1220,12 +1235,13 @@ void colvar::communicate_forces()
return;
}
int grad_index = 0; // index in the scripted gradients, to account for some components being disabled
for (i = 0; i < cvcs.size(); i++) {
if (!cvcs[i]->b_enabled) continue;
cvm::increase_depth();
// 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])->apply_force(colvarvalue(f.as_vector() * func_grads[grad_index++],
cvcs[i]->value().type()));
cvm::decrease_depth();
}
@ -1258,20 +1274,13 @@ void colvar::communicate_forces()
int colvar::set_cvc_flags(std::vector<bool> const &flags) {
size_t i;
if (flags.size() != cvcs.size()) {
cvm::error("ERROR: Wrong number of CVC flags provided.");
return COLVARS_ERROR;
}
bool e = false;
for (i = 0; i < cvcs.size(); i++) {
cvcs[i]->b_enabled = flags[i];
e = e || flags[i];
}
if (!e) {
cvm::error("ERROR: All CVCs are disabled for this colvar.");
return COLVARS_ERROR;
}
// We cannot enable or disable cvcs in the middle of a timestep or colvar evaluation sequence
// so we store the flags that will be enforced at the next call to calc()
cvc_flags = flags;
return COLVARS_OK;
}

3
lib/colvars/colvar.h
View File

@ -514,6 +514,9 @@ protected:
/// \brief Array of \link cvc \endlink objects
std::vector<cvc *> cvcs;
/// \brief Flags to enable or disable cvcs at next colvar evaluation
std::vector<bool> cvc_flags;
/// \brief Initialize the sorted list of atom IDs for atoms involved
/// in all cvcs (called when enabling task_collect_gradients)
void build_atom_list(void);

72
lib/colvars/colvargrid.cpp
View File

@ -24,31 +24,6 @@ colvar_grid_count::colvar_grid_count(std::vector<colvar *> &colvars,
: colvar_grid<size_t>(colvars, def_count, 1)
{}
std::istream & colvar_grid_count::read_restart(std::istream &is)
{
size_t const start_pos = is.tellg();
std::string key, conf;
if ((is >> key) && (key == std::string("grid_parameters"))) {
is.seekg(start_pos, std::ios::beg);
is >> colvarparse::read_block("grid_parameters", conf);
parse_params(conf);
} else {
cvm::log("Grid parameters are missing in the restart file, using those from the configuration.\n");
is.seekg(start_pos, std::ios::beg);
}
read_raw(is);
return is;
}
std::ostream & colvar_grid_count::write_restart(std::ostream &os)
{
write_params(os);
write_raw(os);
return os;
}
colvar_grid_scalar::colvar_grid_scalar()
: colvar_grid<cvm::real>(), samples(NULL), grad(NULL)
{}
@ -79,30 +54,6 @@ colvar_grid_scalar::~colvar_grid_scalar()
}
}
std::istream & colvar_grid_scalar::read_restart(std::istream &is)
{
size_t const start_pos = is.tellg();
std::string key, conf;
if ((is >> key) && (key == std::string("grid_parameters"))) {
is.seekg(start_pos, std::ios::beg);
is >> colvarparse::read_block("grid_parameters", conf);
parse_params(conf);
} else {
cvm::log("Grid parameters are missing in the restart file, using those from the configuration.\n");
is.seekg(start_pos, std::ios::beg);
}
read_raw(is);
return is;
}
std::ostream & colvar_grid_scalar::write_restart(std::ostream &os)
{
write_params(os);
write_raw(os);
return os;
}
cvm::real colvar_grid_scalar::maximum_value() const
{
cvm::real max = data[0];
@ -163,29 +114,6 @@ colvar_grid_gradient::colvar_grid_gradient(std::vector<colvar *> &colvars)
: colvar_grid<cvm::real>(colvars, 0.0, colvars.size()), samples(NULL)
{}
std::istream & colvar_grid_gradient::read_restart(std::istream &is)
{
size_t const start_pos = is.tellg();
std::string key, conf;
if ((is >> key) && (key == std::string("grid_parameters"))) {
is.seekg(start_pos, std::ios::beg);
is >> colvarparse::read_block("grid_parameters", conf);
parse_params(conf);
} else {
cvm::log("Grid parameters are missing in the restart file, using those from the configuration.\n");
is.seekg(start_pos, std::ios::beg);
}
read_raw(is);
return is;
}
std::ostream & colvar_grid_gradient::write_restart(std::ostream &os)
{
write_params(os);
write_raw(os);
return os;
}
void colvar_grid_gradient::write_1D_integral(std::ostream &os)
{
cvm::real bin, min, integral;

44
lib/colvars/colvargrid.h
View File

@ -836,6 +836,32 @@ public:
}
/// \brief Read grid entry in restart file
std::istream & read_restart(std::istream &is)
{
size_t const start_pos = is.tellg();
std::string key, conf;
if ((is >> key) && (key == std::string("grid_parameters"))) {
is.seekg(start_pos, std::ios::beg);
is >> colvarparse::read_block("grid_parameters", conf);
parse_params(conf);
} else {
cvm::log("Grid parameters are missing in the restart file, using those from the configuration.\n");
is.seekg(start_pos, std::ios::beg);
}
read_raw(is);
return is;
}
/// \brief Write grid entry in restart file
std::ostream & write_restart(std::ostream &os)
{
write_params(os);
write_raw(os);
return os;
}
/// \brief Write the grid data without labels, as they are
/// represented in memory
/// \param buf_size Number of values per line
@ -1106,12 +1132,6 @@ public:
return new_data[address(ix) + imult];
}
/// \brief Read the grid from a restart
std::istream & read_restart(std::istream &is);
/// \brief Write the grid to a restart
std::ostream & write_restart(std::ostream &os);
/// \brief Get the value from a formatted output and transform it
/// into the internal representation (it may have been rescaled or
/// manipulated)
@ -1240,12 +1260,6 @@ public:
has_data = true;
}
/// \brief Read the grid from a restart
std::istream & read_restart(std::istream &is);
/// \brief Write the grid to a restart
std::ostream & write_restart(std::ostream &os);
/// \brief Return the highest value
cvm::real maximum_value() const;
@ -1343,12 +1357,6 @@ public:
}
/// \brief Read the grid from a restart
std::istream & read_restart(std::istream &is);
/// \brief Write the grid to a restart
std::ostream & write_restart(std::ostream &os);
/// Compute and return average value for a 1D gradient grid
inline cvm::real average()
{

2
lib/colvars/colvarmodule.h
View File

@ -4,7 +4,7 @@
#define COLVARMODULE_H
#ifndef COLVARS_VERSION
#define COLVARS_VERSION "2015-07-21"
#define COLVARS_VERSION "2015-08-12"
#endif
#ifndef COLVARS_DEBUG