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follow the LAMMPS programming style more closely

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This commit is contained in:
Axel Kohlmeyer
2024-08-05 22:32:55 -04:00
parent 445020359b
commit 46c5ff624c
2 changed files with 77 additions and 72 deletions
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128
src/COLVARS/colvarproxy_lammps.cpp
View File

@ -8,33 +8,25 @@
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.
#include "colvarproxy_lammps.h"
#include <mpi.h>
#include <sys/stat.h>
#include <cerrno>
#include <cstring>
#include <iostream>
#include <memory>
#include <string>
#include "lammps.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "lammps.h" // includes <cstdio>, <mpi.h>, <string>, <vector>
#include "update.h"
#include "utils.h"
#include "random_park.h"
#include "colvarmodule.h"
#include "colvarproxy.h"
#include "colvarproxy_lammps.h"
#include "colvarscript.h"
#define HASH_FAIL -1
/* ---------------------------------------------------------------------- */
colvarproxy_lammps::colvarproxy_lammps(LAMMPS_NS::LAMMPS *lmp)
: _lmp(lmp)
colvarproxy_lammps::colvarproxy_lammps(LAMMPS_NS::LAMMPS *lmp) : _lmp(lmp), _random(nullptr)
{
_random = nullptr;
engine_name_ = "LAMMPS";
first_timestep = true;
@ -47,6 +39,7 @@ colvarproxy_lammps::colvarproxy_lammps(LAMMPS_NS::LAMMPS *lmp)
engine_ready_ = false;
}
/* ---------------------------------------------------------------------- */
void colvarproxy_lammps::init()
{
@ -58,8 +51,7 @@ void colvarproxy_lammps::init()
// Create instance of scripting interface
script = new colvarscript(this, colvars);
cvm::log("Using LAMMPS interface, version "+
cvm::to_str(COLVARPROXY_VERSION)+".\n");
cvm::log("Using LAMMPS interface, version " + cvm::to_str(COLVARPROXY_VERSION) + ".\n");
colvars->cite_feature("LAMMPS engine");
colvars->cite_feature("Colvars-LAMMPS interface");
@ -73,27 +65,28 @@ void colvarproxy_lammps::init()
}
}
/* ---------------------------------------------------------------------- */
colvarproxy_lammps::~colvarproxy_lammps()
{
if (_random) {
delete _random;
}
if (_random) delete _random;
}
/* ---------------------------------------------------------------------- */
void colvarproxy_lammps::set_random_seed(int seed)
{
if (_random) {
delete _random;
}
if (_random) delete _random;
_random = new LAMMPS_NS::RanPark(_lmp, seed);
}
/* ---------------------------------------------------------------------- */
void colvarproxy_lammps::set_replicas_communicator(MPI_Comm root2root)
{
inter_comm = root2root;
// initialize multi-replica support, if available
if (replica_enabled() == COLVARS_OK) {
MPI_Comm_rank(inter_comm, &inter_me);
@ -101,8 +94,10 @@ void colvarproxy_lammps::set_replicas_communicator(MPI_Comm root2root)
}
}
/* ----------------------------------------------------------------------
re-initialize data where needed
------------------------------------------------------------------------- */
// re-initialize data where needed
int colvarproxy_lammps::setup()
{
int error_code = colvarproxy::setup();
@ -113,15 +108,18 @@ int colvarproxy_lammps::setup()
return error_code;
}
// trigger colvars computation
/* ----------------------------------------------------------------------
trigger colvars computation
------------------------------------------------------------------------- */
double colvarproxy_lammps::compute()
{
if (cvm::debug()) {
cvm::log(std::string(cvm::line_marker)+
"colvarproxy_lammps step no. "+
cvm::to_str(_lmp->update->ntimestep)+" [first - last = "+
cvm::to_str(_lmp->update->beginstep)+" - "+
cvm::to_str(_lmp->update->endstep)+"]\n");
cvm::log(std::string(cvm::line_marker) +
"colvarproxy_lammps step no. " +
cvm::to_str(_lmp->update->ntimestep) + " [first - last = " +
cvm::to_str(_lmp->update->beginstep) + " - " +
cvm::to_str(_lmp->update->endstep) + "]\n");
}
if (first_timestep) {
@ -163,40 +161,39 @@ double colvarproxy_lammps::compute()
}
if (cvm::debug()) {
cvm::log(std::string(cvm::line_marker)+
"colvarproxy_lammps, step no. "+cvm::to_str(colvarmodule::it)+"\n"+
cvm::log(std::string(cvm::line_marker) +
"colvarproxy_lammps, step no. " + cvm::to_str(colvarmodule::it) + "\n" +
"Updating internal data.\n");
}
// zero the forces on the atoms, so that they can be accumulated by the colvars
for (size_t i = 0; i < atoms_new_colvar_forces.size(); i++) {
for (size_t i = 0; i < atoms_new_colvar_forces.size(); i++)
atoms_new_colvar_forces[i].reset();
}
bias_energy = 0.0;
if (cvm::debug()) {
cvm::log("atoms_ids = "+cvm::to_str(atoms_ids)+"\n");
cvm::log("atoms_refcount = "+cvm::to_str(atoms_refcount)+"\n");
cvm::log("atoms_positions = "+cvm::to_str(atoms_positions)+"\n");
cvm::log("atoms_new_colvar_forces = "+cvm::to_str(atoms_new_colvar_forces)+"\n");
cvm::log("atoms_ids = " + cvm::to_str(atoms_ids) + "\n");
cvm::log("atoms_refcount = " + cvm::to_str(atoms_refcount) + "\n");
cvm::log("atoms_positions = " + cvm::to_str(atoms_positions) + "\n");
cvm::log("atoms_new_colvar_forces = " + cvm::to_str(atoms_new_colvar_forces) + "\n");
}
// Call the collective variable module
if (colvars->calc() != COLVARS_OK) {
if (colvars->calc() != COLVARS_OK)
cvm::error("Error in the collective variables module.\n", COLVARS_ERROR);
}
if (cvm::debug()) {
cvm::log("atoms_ids = "+cvm::to_str(atoms_ids)+"\n");
cvm::log("atoms_refcount = "+cvm::to_str(atoms_refcount)+"\n");
cvm::log("atoms_positions = "+cvm::to_str(atoms_positions)+"\n");
cvm::log("atoms_new_colvar_forces = "+cvm::to_str(atoms_new_colvar_forces)+"\n");
cvm::log("atoms_ids = " + cvm::to_str(atoms_ids) + "\n");
cvm::log("atoms_refcount = " + cvm::to_str(atoms_refcount) + "\n");
cvm::log("atoms_positions = " + cvm::to_str(atoms_positions) + "\n");
cvm::log("atoms_new_colvar_forces = " + cvm::to_str(atoms_new_colvar_forces) + "\n");
}
return bias_energy;
}
/* ---------------------------------------------------------------------- */
cvm::rvector colvarproxy_lammps::position_distance(cvm::atom_pos const &pos1,
cvm::atom_pos const &pos2)
@ -209,6 +206,7 @@ cvm::rvector colvarproxy_lammps::position_distance(cvm::atom_pos const &pos1,
return {xtmp, ytmp, ztmp};
}
/* ---------------------------------------------------------------------- */
void colvarproxy_lammps::log(std::string const &message)
{
@ -217,14 +215,15 @@ void colvarproxy_lammps::log(std::string const &message)
LAMMPS_NS::utils::logmesg(_lmp, message);
}
/* ---------------------------------------------------------------------- */
void colvarproxy_lammps::error(std::string const &message)
{
log(message);
_lmp->error->one(FLERR,
"Fatal error in the collective variables module.\n");
_lmp->error->one(FLERR, "Fatal error in the collective variables module");
}
/* ---------------------------------------------------------------------- */
char const *colvarproxy_lammps::script_obj_to_str(unsigned char *obj)
{
@ -232,6 +231,7 @@ char const *colvarproxy_lammps::script_obj_to_str(unsigned char *obj)
return reinterpret_cast<char *>(obj);
}
/* ---------------------------------------------------------------------- */
std::vector<std::string> colvarproxy_lammps::script_obj_to_str_vector(unsigned char *obj)
{
@ -242,47 +242,52 @@ std::vector<std::string> colvarproxy_lammps::script_obj_to_str_vector(unsigned c
return LAMMPS_NS::utils::split_words(input); // :-)))
}
/* ---------------------------------------------------------------------- */
int colvarproxy_lammps::set_unit_system(std::string const &units_in, bool /*check_only*/)
{
std::string lmp_units = _lmp->update->unit_style;
if (units_in != lmp_units) {
cvm::error("Error: Specified unit system for Colvars \"" + units_in + "\" is incompatible with LAMMPS internal units (" + lmp_units + ").\n");
cvm::error("Error: Specified unit system for Colvars \"" + units_in +
"\" is incompatible with LAMMPS internal units (" + lmp_units + ").\n");
return COLVARS_ERROR;
}
return COLVARS_OK;
}
// multi-replica support
/* ----------------------------------------------------------------------
multi-replica support
------------------------------------------------------------------------- */
int colvarproxy_lammps::replica_enabled()
{
return (inter_comm != MPI_COMM_NULL) ? COLVARS_OK : COLVARS_NOT_IMPLEMENTED;
}
/* ---------------------------------------------------------------------- */
int colvarproxy_lammps::replica_index()
{
return inter_me;
}
/* ---------------------------------------------------------------------- */
int colvarproxy_lammps::num_replicas()
{
return inter_num;
}
/* ---------------------------------------------------------------------- */
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)
int colvarproxy_lammps::replica_comm_recv(char* msg_data, int buf_len, int src_rep)
{
MPI_Status status;
int retval;
@ -294,9 +299,9 @@ int colvarproxy_lammps::replica_comm_recv(char* msg_data,
return retval;
}
/* ---------------------------------------------------------------------- */
int colvarproxy_lammps::replica_comm_send(char* msg_data,
int msg_len, int dest_rep)
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);
@ -306,26 +311,26 @@ int colvarproxy_lammps::replica_comm_send(char* msg_data,
return retval;
}
/* ---------------------------------------------------------------------- */
int colvarproxy_lammps::check_atom_id(int atom_number)
{
int const aid = atom_number;
if (cvm::debug())
log("Adding atom "+cvm::to_str(atom_number)+
" for collective variables calculation.\n");
log("Adding atom " + cvm::to_str(atom_number) + " for collective variables calculation.\n");
// TODO add upper boundary check?
if ((aid < 0)) {
cvm::error("Error: invalid atom number specified, "+
cvm::to_str(atom_number)+"\n", COLVARS_INPUT_ERROR);
cvm::error("Error: invalid atom number specified, " +
cvm::to_str(atom_number) + "\n", COLVARS_INPUT_ERROR);
return COLVARS_INPUT_ERROR;
}
return aid;
}
/* ---------------------------------------------------------------------- */
int colvarproxy_lammps::init_atom(int atom_number)
{
@ -340,9 +345,7 @@ int colvarproxy_lammps::init_atom(int atom_number)
}
aid = check_atom_id(atom_number);
if (aid < 0) {
return aid;
}
if (aid < 0) return aid;
int const index = colvarproxy::add_atom_slot(aid);
// add entries for the LAMMPS-specific fields
@ -350,4 +353,3 @@ int colvarproxy_lammps::init_atom(int atom_number)
return index;
}

21
src/COLVARS/colvarproxy_lammps.h
View File

@ -16,11 +16,15 @@
#include "colvarproxy.h"
#include "colvartypes.h"
#include "domain.h" // IWYU pragma: keep
#include "force.h" // IWYU pragma: keep
#include "lammps.h" // IWYU pragma: keep
#include <mpi.h>
#include "random_park.h"
#include "update.h" // IWYU pragma: keep
// forward declarations
namespace LAMMPS_NS {
class LAMMPS;
} // namespace LAMMPS_NS
/// \brief Communication between colvars and LAMMPS
/// (implementation of \link colvarproxy \endlink)
@ -48,7 +52,6 @@ class colvarproxy_lammps : public colvarproxy {
friend class cvm::atom;
colvarproxy_lammps(LAMMPS_NS::LAMMPS *lmp);
~colvarproxy_lammps() override;
void init();
@ -63,12 +66,11 @@ class colvarproxy_lammps : public colvarproxy {
// disable default and copy constructor
private:
colvarproxy_lammps(){};
colvarproxy_lammps(const colvarproxy_lammps &){};
colvarproxy_lammps() {};
colvarproxy_lammps(const colvarproxy_lammps &) {};
// methods for lammps to move data or trigger actions in the proxy
public:
bool total_forces_enabled() const override { return total_force_requested; };
bool total_forces_same_step() const override { return true; };
bool want_exit() const { return do_exit; };
@ -91,7 +93,8 @@ class colvarproxy_lammps : public colvarproxy {
void log(std::string const &message) override;
void error(std::string const &message) override;
cvm::rvector position_distance(cvm::atom_pos const &pos1, cvm::atom_pos const &pos2) const override;
cvm::rvector position_distance(cvm::atom_pos const &pos1,
cvm::atom_pos const &pos2) const override;
cvm::real rand_gaussian(void) override { return _random->gaussian(); };