Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/src/USER-COLVARS/colvarproxy_lammps.cpp
354e20f43157lammm-master-deprecated

Last Change
Raw File

colvarproxy_lammps.cpp
View Options

#include <mpi.h>
#include "lammps.h"
#include "atom.h"
#include "error.h"
#include "output.h"
#include "random_park.h"
#include "fix_colvars.h"
#include "colvarmodule.h"
#include "colvaratoms.h"
#include "colvarproxy.h"
#include "colvarproxy_lammps.h"
#include <sys/types.h>
#include <sys/stat.h>
#include <unistd.h>
#include <cerrno>
#include <cstdio>
#include <cstring>
#include <iostream>
#include <sstream>
#include <string>
#define HASH_FAIL -1
////////////////////////////////////////////////////////////////////////
// local helper functions
// safely move filename to filename.extension
static int my_backup_file(const char *filename, const char *extension)
{
struct stat sbuf;
if (stat(filename, &sbuf) == 0) {
if (!extension) extension = ".BAK";
char *backup = new char[strlen(filename)+strlen(extension)+1];
strcpy(backup, filename);
strcat(backup, extension);
#if defined(_WIN32) && !defined(__CYGWIN__)
remove(backup);
#endif
if (rename(filename,backup)) {
char *sys_err_msg = strerror(errno);
if (!sys_err_msg) sys_err_msg = (char *) "(unknown error)";
fprintf(stderr,"Error renaming file %s to %s: %s\n",
filename, backup, sys_err_msg);
delete [] backup;
return COLVARS_ERROR;
}
delete [] backup;
}
return COLVARS_OK;
}
////////////////////////////////////////////////////////////////////////
colvarproxy_lammps::colvarproxy_lammps(LAMMPS_NS::LAMMPS *lmp,
const char *inp_name,
const char *out_name,
const int seed,
const double temp,
MPI_Comm root2root)
: _lmp(lmp), inter_comm(root2root)
{
if (cvm::debug())
log("Initializing the colvars proxy object.\n");
_random = new LAMMPS_NS::RanPark(lmp,seed);
first_timestep=true;
system_force_requested=false;
previous_step=-1;
t_target=temp;
do_exit=false;
restart_every=0;
// User-scripted forces are not available in LAMMPS
force_script_defined = false;
have_scripts = false;
// set input restart name and strip the extension, if present
input_prefix_str = std::string(inp_name ? inp_name : "");
if (input_prefix_str.rfind(".colvars.state") != std::string::npos)
input_prefix_str.erase(input_prefix_str.rfind(".colvars.state"),
std::string(".colvars.state").size());
// output prefix is always given
output_prefix_str = std::string(out_name);
// not so for restarts
restart_output_prefix_str = std::string("rest");
// check if it is possible to save output configuration
if ((!output_prefix_str.size()) && (!restart_output_prefix_str.size())) {
fatal_error("Error: neither the final output state file or "
"the output restart file could be defined, exiting.\n");
}
// try to extract a restart prefix from a potential restart command.
LAMMPS_NS::Output *outp = _lmp->output;
if ((outp->restart_every_single > 0) && (outp->restart1 != 0)) {
restart_output_prefix_str = std::string(outp->restart1);
} else if ((outp->restart_every_double > 0) && (outp->restart2a != 0)) {
restart_output_prefix_str = std::string(outp->restart2a);
}
// trim off unwanted stuff from the restart prefix
if (restart_output_prefix_str.rfind(".*") != std::string::npos)
restart_output_prefix_str.erase(restart_output_prefix_str.rfind(".*"),2);
// initialize multi-replica support, if available
if (replica_enabled()) {
MPI_Comm_rank(inter_comm, &inter_me);
MPI_Comm_size(inter_comm, &inter_num);
}
}
void colvarproxy_lammps::init(const char *conf_file)
{
// create the colvarmodule instance
colvars = new colvarmodule(this);
cvm::log("Using LAMMPS interface, version "+
cvm::to_str(COLVARPROXY_VERSION)+".\n");
my_angstrom = _lmp->force->angstrom;
my_boltzmann = _lmp->force->boltz;
my_timestep = _lmp->update->dt * _lmp->force->femtosecond;
// TODO move one or more of these to setup() if needed
colvars->read_config_file(conf_file);
colvars->setup_input();
colvars->setup_output();
if (_lmp->update->ntimestep != 0) {
cvm::log("Initializing step number as firstTimestep.\n");
colvars->it = colvars->it_restart = _lmp->update->ntimestep;
}
if (cvm::debug()) {
log("colvars_atoms = "+cvm::to_str(colvars_atoms)+"\n");
log("colvars_atoms_ncopies = "+cvm::to_str(colvars_atoms_ncopies)+"\n");
log("positions = "+cvm::to_str(positions)+"\n");
log("applied_forces = "+cvm::to_str(applied_forces)+"\n");
log(cvm::line_marker);
log("Info: done initializing the colvars proxy object.\n");
}
}
colvarproxy_lammps::~colvarproxy_lammps()
{
delete _random;
if (colvars != NULL) {
colvars->write_output_files();
delete colvars;
colvars = NULL;
}
}
// re-initialize data where needed
void colvarproxy_lammps::setup()
{
my_timestep = _lmp->update->dt * _lmp->force->femtosecond;
colvars->setup();
}
// trigger colvars computation
double colvarproxy_lammps::compute()
{
if (first_timestep) {
first_timestep = false;
} else {
// Use the time step number inherited from LAMMPS
if ( _lmp->update->ntimestep - previous_step == 1 )
colvars->it++;
// Other cases could mean:
// - run 0
// - beginning of a new run statement
// then the internal counter should not be incremented
}
previous_step = _lmp->update->ntimestep;
if (cvm::debug()) {
cvm::log(cvm::line_marker+
"colvarproxy_lammps, step no. "+cvm::to_str(colvars->it)+"\n"+
"Updating internal data.\n");
}
// backup applied forces if necessary to calculate system forces
if (system_force_requested)
previous_applied_forces = applied_forces;
// zero the forces on the atoms, so that they can be accumulated by the colvars
for (size_t i = 0; i < applied_forces.size(); i++) {
applied_forces[i].x = applied_forces[i].y = applied_forces[i].z = 0.0;
}
bias_energy = 0.0;
// call the collective variable module
colvars->calc();
#if 0
for (int i=0; i < colvars_atoms.size(); ++i) {
fprintf(stderr,"CV: atom %d/%d/%d pos: %g %g %g for: %g %g %g\n",
colvars_atoms[i], colvars_atoms_ncopies[i],
positions[i].type, positions[i].x, positions[i].y, positions[i].z,
applied_forces[i].x, applied_forces[i].y, applied_forces[i].z);
}
#endif
return bias_energy;
}
void colvarproxy_lammps::serialize_status(std::string &rst)
{
std::ostringstream os;
colvars->write_restart(os);
rst = os.str();
}
// set status from string
bool colvarproxy_lammps::deserialize_status(std::string &rst)
{
std::istringstream is;
is.str(rst);
if (!colvars->read_restart(is)) {
return false;
} else {
return true;
}
}
cvm::rvector colvarproxy_lammps::position_distance(cvm::atom_pos const &pos1,
cvm::atom_pos const &pos2)
{
double xtmp = pos2.x - pos1.x;
double ytmp = pos2.y - pos1.y;
double ztmp = pos2.z - pos1.z;
_lmp->domain->minimum_image(xtmp,ytmp,ztmp);
return cvm::rvector(xtmp, ytmp, ztmp);
}
cvm::real colvarproxy_lammps::position_dist2(cvm::atom_pos const &pos1,
cvm::atom_pos const &pos2)
{
double xtmp = pos2.x - pos1.x;
double ytmp = pos2.y - pos1.y;
double ztmp = pos2.z - pos1.z;
_lmp->domain->minimum_image(xtmp,ytmp,ztmp);
return cvm::real(xtmp*xtmp + ytmp*ytmp + ztmp*ztmp);
}
inline void colvarproxy_lammps::select_closest_image(cvm::atom_pos &pos,
cvm::atom_pos const &ref)
{
double xtmp = pos.x - ref.x;
double ytmp = pos.y - ref.y;
double ztmp = pos.z - ref.z;
_lmp->domain->minimum_image(xtmp,ytmp,ztmp);
pos.x = ref.x + xtmp;
pos.y = ref.y + ytmp;
pos.z = ref.z + ztmp;
}
void colvarproxy_lammps::log(std::string const &message)
{
std::istringstream is(message);
std::string line;
while (std::getline(is, line)) {
if (_lmp->screen)
fprintf(_lmp->screen,"colvars: %s\n",line.c_str());
if (_lmp->logfile)
fprintf(_lmp->logfile,"colvars: %s\n",line.c_str());
}
}
void colvarproxy_lammps::error(std::string const &message)
{
// In LAMMPS, all errors are fatal
fatal_error(message);
}
void colvarproxy_lammps::fatal_error(std::string const &message)
{
log(message);
if (!cvm::debug())
log("If this error message is unclear, try recompiling the "
"colvars library and LAMMPS with -DCOLVARS_DEBUG.\n");
_lmp->error->one(FLERR,
"Fatal error in the collective variables module.\n");
}
void colvarproxy_lammps::exit(std::string const &message)
{
log(message);
log("Request to exit the simulation made.\n");
do_exit=true;
}
enum e_pdb_field {
e_pdb_none,
e_pdb_occ,
e_pdb_beta,
e_pdb_x,
e_pdb_y,
e_pdb_z,
e_pdb_ntot
};
e_pdb_field pdb_field_str2enum(std::string const &pdb_field_str)
{
e_pdb_field pdb_field = e_pdb_none;
if (colvarparse::to_lower_cppstr(pdb_field_str) ==
colvarparse::to_lower_cppstr("O")) {
pdb_field = e_pdb_occ;
}
if (colvarparse::to_lower_cppstr(pdb_field_str) ==
colvarparse::to_lower_cppstr("B")) {
pdb_field = e_pdb_beta;
}
if (colvarparse::to_lower_cppstr(pdb_field_str) ==
colvarparse::to_lower_cppstr("X")) {
pdb_field = e_pdb_x;
}
if (colvarparse::to_lower_cppstr(pdb_field_str) ==
colvarparse::to_lower_cppstr("Y")) {
pdb_field = e_pdb_y;
}
if (colvarparse::to_lower_cppstr(pdb_field_str) ==
colvarparse::to_lower_cppstr("Z")) {
pdb_field = e_pdb_z;
}
if (pdb_field == e_pdb_none) {
cvm::fatal_error("Error: unsupported PDB field, \""+
pdb_field_str+"\".\n");
}
return pdb_field;
}
int colvarproxy_lammps::load_coords(char const *pdb_filename,
std::vector<cvm::atom_pos> &pos,
const std::vector<int> &indices,
std::string const &pdb_field_str,
double const pdb_field_value)
{
cvm::fatal_error("Reading collective variable coordinates "
"from a PDB file is currently not supported.\n");
return COLVARS_ERROR;
}
int colvarproxy_lammps::load_atoms(char const *pdb_filename,
std::vector<cvm::atom> &atoms,
std::string const &pdb_field_str,
double const pdb_field_value)
{
cvm::fatal_error("Selecting collective variable atoms "
"from a PDB file is currently not supported.\n");
return COLVARS_ERROR;
}
int colvarproxy_lammps::backup_file(char const *filename)
{
if (std::string(filename).rfind(std::string(".colvars.state"))
!= std::string::npos) {
return my_backup_file(filename, ".old");
} else {
return my_backup_file(filename, ".BAK");
}
}
int colvarproxy_lammps::init_lammps_atom(const int &aid, cvm::atom *atom)
{
atom->id = aid;
atom->mass = 0.0;
for (size_t i = 0; i < colvars_atoms.size(); i++) {
if (colvars_atoms[i] == aid) {
// this atom id was already recorded
colvars_atoms_ncopies[i] += 1;
return i;
}
}
// allocate a new slot for this atom
colvars_atoms_ncopies.push_back(1);
colvars_atoms.push_back(aid);
struct commdata c;
c.tag = aid;
c.type = 0;
c.x = c.y = c.z = 0.0;
positions.push_back(c);
total_forces.push_back(c);
applied_forces.push_back(c);
return colvars_atoms.size()-1;
}
// multi-replica support
void colvarproxy_lammps::replica_comm_barrier() {
MPI_Barrier(inter_comm);
}
int colvarproxy_lammps::replica_comm_recv(char* msg_data,
int buf_len, int src_rep)
{
MPI_Status status;
int retval;
retval = MPI_Recv(msg_data,buf_len,MPI_CHAR,src_rep,0,inter_comm,&status);
if (retval == MPI_SUCCESS) {
MPI_Get_count(&status, MPI_CHAR, &retval);
} else retval = 0;
return retval;
}
int colvarproxy_lammps::replica_comm_send(char* msg_data,
int msg_len, int dest_rep)
{
int retval;
retval = MPI_Send(msg_data,msg_len,MPI_CHAR,dest_rep,0,inter_comm);
if (retval == MPI_SUCCESS) {
retval = msg_len;
} else retval = 0;
return retval;
}
// atom member functions, LAMMPS specific implementations
cvm::atom::atom(const int &id)
{
if (cvm::debug())
cvm::log("Adding atom "+cvm::to_str(id)+
" for collective variables calculation.\n");
if (id < 0)
cvm::fatal_error("Error: invalid atom ID specified, "+
cvm::to_str(id)+"\n");
int idx = ((colvarproxy_lammps *) cvm::proxy)->init_lammps_atom(id,this);
if (idx < 0)
cvm::fatal_error("Error: atom ID , "+cvm::to_str(id)+" does not exist.\n");
this->index = idx;
if (cvm::debug())
cvm::log("The index of this atom in the colvarproxy_lammps arrays is "+
cvm::to_str(this->index)+".\n");
this->reset_data();
}
/// For AMBER topologies, the segment id is automatically set to
/// "MAIN" (the segment id assigned by NAMD's AMBER topology parser),
/// and is therefore optional when an AMBER topology is used
cvm::atom::atom(cvm::residue_id const &residue,
std::string const &atom_name,
std::string const &segment_id)
{
cvm::fatal_error("Creating collective variable atoms "
"from a PDB file is currently not supported.\n");
}
// copy constructor
cvm::atom::atom(cvm::atom const &a)
: index(a.index), id(a.id), mass(a.mass)
{
// init_lammps_atom() has already been called by a's constructor, no
// need to call it again
// need to increment the counter anyway
colvarproxy_lammps *cp = (colvarproxy_lammps *) cvm::proxy;
cp->colvars_atoms_ncopies[this->index] += 1;
}
cvm::atom::~atom()
{
if (this->index >= 0) {
colvarproxy_lammps *cp = (colvarproxy_lammps *) cvm::proxy;
if (cp->colvars_atoms_ncopies[this->index] > 0)
cp->colvars_atoms_ncopies[this->index] -= 1;
}
}
void cvm::atom::read_position()
{
colvarproxy_lammps const * const cp = (colvarproxy_lammps *) cvm::proxy;
this->pos.x = cp->positions[this->index].x;
this->pos.y = cp->positions[this->index].y;
this->pos.z = cp->positions[this->index].z;
this->mass = cp->positions[this->index].m;
}
void cvm::atom::read_velocity()
{
cvm::fatal_error("Error: read_velocity is not yet implemented.\n");
}
void cvm::atom::read_system_force()
{
colvarproxy_lammps const * const cp = (colvarproxy_lammps *) cvm::proxy;
this->system_force.x = cp->total_forces[this->index].x
- cp->previous_applied_forces[this->index].x;
this->system_force.y = cp->total_forces[this->index].y
- cp->previous_applied_forces[this->index].y;
this->system_force.z = cp->total_forces[this->index].z
- cp->previous_applied_forces[this->index].z;
}
void cvm::atom::apply_force(cvm::rvector const &new_force)
{
colvarproxy_lammps *cp = (colvarproxy_lammps *) cvm::proxy;
cp->applied_forces[this->index].x += new_force.x;
cp->applied_forces[this->index].y += new_force.y;
cp->applied_forces[this->index].z += new_force.z;
}
c4science · Help