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colvarproxy.cpp
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Sun, May 12, 05:30

colvarproxy.cpp
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// -*- c++ -*-
// This file is part of the Collective Variables module (Colvars).
// The original version of Colvars and its updates are located at:
// https://github.com/colvars/colvars
// Please update all Colvars source files before making any changes.
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.
#include <sstream>
#include <string.h>
#include "colvarmodule.h"
#include "colvarproxy.h"
#include "colvarscript.h"
#include "colvaratoms.h"
colvarproxy_system::colvarproxy_system() {}
colvarproxy_system::~colvarproxy_system() {}
void colvarproxy_system::add_energy(cvm::real energy) {}
void colvarproxy_system::request_total_force(bool yesno)
{
if (yesno == true)
cvm::error("Error: total forces are currently not implemented.\n",
COLVARS_NOT_IMPLEMENTED);
}
bool colvarproxy_system::total_forces_enabled() const
{
return false;
}
cvm::real colvarproxy_system::position_dist2(cvm::atom_pos const &pos1,
cvm::atom_pos const &pos2)
{
return (position_distance(pos1, pos2)).norm2();
}
colvarproxy_atoms::colvarproxy_atoms() {}
colvarproxy_atoms::~colvarproxy_atoms()
{
reset();
}
int colvarproxy_atoms::reset()
{
atoms_ids.clear();
atoms_ncopies.clear();
atoms_masses.clear();
atoms_charges.clear();
atoms_positions.clear();
atoms_total_forces.clear();
atoms_new_colvar_forces.clear();
return COLVARS_OK;
}
int colvarproxy_atoms::add_atom_slot(int atom_id)
{
atoms_ids.push_back(atom_id);
atoms_ncopies.push_back(1);
atoms_masses.push_back(1.0);
atoms_charges.push_back(0.0);
atoms_positions.push_back(cvm::rvector(0.0, 0.0, 0.0));
atoms_total_forces.push_back(cvm::rvector(0.0, 0.0, 0.0));
atoms_new_colvar_forces.push_back(cvm::rvector(0.0, 0.0, 0.0));
return (atoms_ids.size() - 1);
}
int colvarproxy_atoms::init_atom(cvm::residue_id const &residue,
std::string const &atom_name,
std::string const &segment_id)
{
cvm::error("Error: initializing an atom by name and residue number is currently not supported.\n",
COLVARS_NOT_IMPLEMENTED);
return COLVARS_NOT_IMPLEMENTED;
}
int colvarproxy_atoms::check_atom_id(cvm::residue_id const &residue,
std::string const &atom_name,
std::string const &segment_id)
{
colvarproxy_atoms::init_atom(residue, atom_name, segment_id);
return COLVARS_NOT_IMPLEMENTED;
}
void colvarproxy_atoms::clear_atom(int index)
{
if (((size_t) index) >= atoms_ids.size()) {
cvm::error("Error: trying to disable an atom that was not previously requested.\n",
INPUT_ERROR);
}
if (atoms_ncopies[index] > 0) {
atoms_ncopies[index] -= 1;
}
}
int colvarproxy_atoms::load_atoms(char const *filename,
cvm::atom_group &atoms,
std::string const &pdb_field,
double const)
{
return cvm::error("Error: loading atom identifiers from a file "
"is currently not implemented.\n",
COLVARS_NOT_IMPLEMENTED);
}
int colvarproxy_atoms::load_coords(char const *filename,
std::vector<cvm::atom_pos> &pos,
const std::vector<int> &indices,
std::string const &pdb_field,
double const)
{
return cvm::error("Error: loading atomic coordinates from a file "
"is currently not implemented.\n",
COLVARS_NOT_IMPLEMENTED);
}
colvarproxy_atom_groups::colvarproxy_atom_groups() {}
colvarproxy_atom_groups::~colvarproxy_atom_groups()
{
reset();
}
int colvarproxy_atom_groups::reset()
{
atom_groups_ids.clear();
atom_groups_ncopies.clear();
atom_groups_masses.clear();
atom_groups_charges.clear();
atom_groups_coms.clear();
atom_groups_total_forces.clear();
atom_groups_new_colvar_forces.clear();
return COLVARS_OK;
}
int colvarproxy_atom_groups::add_atom_group_slot(int atom_group_id)
{
atom_groups_ids.push_back(atom_group_id);
atom_groups_ncopies.push_back(1);
atom_groups_masses.push_back(1.0);
atom_groups_charges.push_back(0.0);
atom_groups_coms.push_back(cvm::rvector(0.0, 0.0, 0.0));
atom_groups_total_forces.push_back(cvm::rvector(0.0, 0.0, 0.0));
atom_groups_new_colvar_forces.push_back(cvm::rvector(0.0, 0.0, 0.0));
return (atom_groups_ids.size() - 1);
}
int colvarproxy_atom_groups::scalable_group_coms()
{
return COLVARS_NOT_IMPLEMENTED;
}
int colvarproxy_atom_groups::init_atom_group(std::vector<int> const &atoms_ids)
{
cvm::error("Error: initializing a group outside of the Colvars module "
"is currently not supported.\n",
COLVARS_NOT_IMPLEMENTED);
return COLVARS_NOT_IMPLEMENTED;
}
void colvarproxy_atom_groups::clear_atom_group(int index)
{
if (((size_t) index) >= atom_groups_ids.size()) {
cvm::error("Error: trying to disable an atom group "
"that was not previously requested.\n",
INPUT_ERROR);
}
if (atom_groups_ncopies[index] > 0) {
atom_groups_ncopies[index] -= 1;
}
}
colvarproxy_smp::colvarproxy_smp()
{
b_smp_active = true;
}
colvarproxy_smp::~colvarproxy_smp() {}
int colvarproxy_smp::smp_enabled()
{
return COLVARS_NOT_IMPLEMENTED;
}
int colvarproxy_smp::smp_colvars_loop()
{
return COLVARS_NOT_IMPLEMENTED;
}
int colvarproxy_smp::smp_biases_loop()
{
return COLVARS_NOT_IMPLEMENTED;
}
int colvarproxy_smp::smp_biases_script_loop()
{
return COLVARS_NOT_IMPLEMENTED;
}
int colvarproxy_smp::smp_thread_id()
{
return COLVARS_NOT_IMPLEMENTED;
}
int colvarproxy_smp::smp_num_threads()
{
return COLVARS_NOT_IMPLEMENTED;
}
int colvarproxy_smp::smp_lock()
{
return COLVARS_OK;
}
int colvarproxy_smp::smp_trylock()
{
return COLVARS_OK;
}
int colvarproxy_smp::smp_unlock()
{
return COLVARS_OK;
}
colvarproxy_replicas::colvarproxy_replicas() {}
colvarproxy_replicas::~colvarproxy_replicas() {}
bool colvarproxy_replicas::replica_enabled()
{
return false;
}
int colvarproxy_replicas::replica_index()
{
return 0;
}
int colvarproxy_replicas::replica_num()
{
return 1;
}
void colvarproxy_replicas::replica_comm_barrier() {}
int colvarproxy_replicas::replica_comm_recv(char* msg_data,
int buf_len,
int src_rep)
{
return COLVARS_NOT_IMPLEMENTED;
}
int colvarproxy_replicas::replica_comm_send(char* msg_data,
int msg_len,
int dest_rep)
{
return COLVARS_NOT_IMPLEMENTED;
}
colvarproxy_script::colvarproxy_script()
{
script = NULL;
}
colvarproxy_script::~colvarproxy_script() {}
char *colvarproxy_script::script_obj_to_str(unsigned char *obj)
{
return reinterpret_cast<char *>(obj);
}
int colvarproxy_script::run_force_callback()
{
return COLVARS_NOT_IMPLEMENTED;
}
int colvarproxy_script::run_colvar_callback(
std::string const &name,
std::vector<const colvarvalue *> const &cvcs,
colvarvalue &value)
{
return COLVARS_NOT_IMPLEMENTED;
}
int colvarproxy_script::run_colvar_gradient_callback(
std::string const &name,
std::vector<const colvarvalue *> const &cvcs,
std::vector<cvm::matrix2d<cvm::real> > &gradient)
{
return COLVARS_NOT_IMPLEMENTED;
}
colvarproxy_io::colvarproxy_io() {}
colvarproxy_io::~colvarproxy_io() {}
int colvarproxy_io::get_frame(long int&)
{
return COLVARS_NOT_IMPLEMENTED;
}
int colvarproxy_io::set_frame(long int)
{
return COLVARS_NOT_IMPLEMENTED;
}
std::ostream * colvarproxy_io::output_stream(std::string const &output_name,
std::ios_base::openmode mode)
{
if (cvm::debug()) {
cvm::log("Using colvarproxy::output_stream()\n");
}
std::list<std::ostream *>::iterator osi = output_files.begin();
std::list<std::string>::iterator osni = output_stream_names.begin();
for ( ; osi != output_files.end(); osi++, osni++) {
if (*osni == output_name) {
return *osi;
}
}
if (!(mode & (std::ios_base::app | std::ios_base::ate))) {
backup_file(output_name);
}
std::ofstream *os = new std::ofstream(output_name.c_str(), mode);
if (!os->is_open()) {
cvm::error("Error: cannot write to file/channel \""+output_name+"\".\n",
FILE_ERROR);
return NULL;
}
output_stream_names.push_back(output_name);
output_files.push_back(os);
return os;
}
int colvarproxy_io::flush_output_stream(std::ostream *os)
{
std::list<std::ostream *>::iterator osi = output_files.begin();
std::list<std::string>::iterator osni = output_stream_names.begin();
for ( ; osi != output_files.end(); osi++, osni++) {
if (*osi == os) {
((std::ofstream *) (*osi))->flush();
return COLVARS_OK;
}
}
return cvm::error("Error: trying to flush an output file/channel "
"that wasn't open.\n", BUG_ERROR);
}
int colvarproxy_io::close_output_stream(std::string const &output_name)
{
std::list<std::ostream *>::iterator osi = output_files.begin();
std::list<std::string>::iterator osni = output_stream_names.begin();
for ( ; osi != output_files.end(); osi++, osni++) {
if (*osni == output_name) {
((std::ofstream *) (*osi))->close();
output_files.erase(osi);
output_stream_names.erase(osni);
return COLVARS_OK;
}
}
return cvm::error("Error: trying to close an output file/channel "
"that wasn't open.\n", BUG_ERROR);
}
int colvarproxy_io::backup_file(char const *filename)
{
return COLVARS_NOT_IMPLEMENTED;
}
colvarproxy::colvarproxy()
{
colvars = NULL;
b_simulation_running = true;
}
colvarproxy::~colvarproxy() {}
int colvarproxy::reset()
{
int error_code = COLVARS_OK;
error_code |= colvarproxy_atoms::reset();
error_code |= colvarproxy_atom_groups::reset();
return error_code;
}
int colvarproxy::setup()
{
return COLVARS_OK;
}
int colvarproxy::update_input()
{
return COLVARS_OK;
}
int colvarproxy::update_output()
{
return COLVARS_OK;
}
size_t colvarproxy::restart_frequency()
{
return 0;
}

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