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remove files autogenerated upon build

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yotamfe
2024-10-09 11:57:45 +03:00
parent 54e7a8a4c7
commit 85a0b668c3
4 changed files with 0 additions and 346 deletions
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122
src/fix_pimdb_langevin.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Package FixPIMDBLangevin
Purpose TODO
Copyright TODO
Authors TODO
Updated TODO
Version 1.0
------------------------------------------------------------------------- */
#include <cmath>
#include <cstring>
#include <cstdlib>
#include <chrono>
#include <iostream>
#include <fstream>
#include "fix_pimdb_langevin.h"
#include "universe.h"
#include "comm.h"
#include "force.h"
#include "atom.h"
#include "domain.h"
#include "update.h"
#include "memory.h"
#include "error.h"
#include <algorithm>
using namespace LAMMPS_NS;
using namespace FixConst;
enum{PIMD,NMPIMD,CMD};
/* ---------------------------------------------------------------------- */
FixPIMDBLangevin::FixPIMDBLangevin(LAMMPS *lmp, int narg, char **arg) :
FixPIMDLangevin(lmp, narg, arg),
bosonic_exchange(lmp, atom->nlocal, np, universe->me,
false)
{
if (method != PIMD) {
error->universe_all(FLERR, "Method not supported in fix pimdb/langevin; only method PIMD");
}
size_vector = 6;
nbosons = atom->nlocal;
memory->create(f_tag_order, nbosons, 3, "FixPIMDBLangevin:f_tag_order");
}
/* ---------------------------------------------------------------------- */
FixPIMDBLangevin::~FixPIMDBLangevin() {
memory->destroy(f_tag_order);
}
/* ---------------------------------------------------------------------- */
void FixPIMDBLangevin::spring_force() {
double ff = fbond * atom->mass[atom->type[0]]; // TODO: ensure that all masses are the same
int nlocal = atom->nlocal;
double* me_bead_positions = *(atom->x);
double* last_bead_positions = &bufsortedall[x_last * nlocal][0];
double* next_bead_positions = &bufsortedall[x_next * nlocal][0];
bosonic_exchange.prepare_with_coordinates(me_bead_positions,
last_bead_positions, next_bead_positions,
beta_np, 1 / beta, ff);
for (int i = 0; i < nbosons; i++) {
f_tag_order[i][0] = 0.0;
f_tag_order[i][1] = 0.0;
f_tag_order[i][2] = 0.0;
}
bosonic_exchange.spring_force(f_tag_order);
double** f = atom->f;
tagint* tag = atom->tag;
for (int i = 0; i < nbosons; i++) {
f[i][0] += f_tag_order[tag[i] - 1][0];
f[i][1] += f_tag_order[tag[i] - 1][1];
f[i][2] += f_tag_order[tag[i] - 1][2];
}
}
/* ---------------------------------------------------------------------- */
void FixPIMDBLangevin::compute_spring_energy() {
total_spring_energy = bosonic_exchange.get_potential();
se_bead = (universe->iworld == np - 1 ? total_spring_energy : 0.0);
}
/* ---------------------------------------------------------------------- */
void FixPIMDBLangevin::compute_t_prim()
{
if (universe->iworld == 0)
t_prim = bosonic_exchange.prim_estimator();
}
/* ---------------------------------------------------------------------- */
double FixPIMDBLangevin::compute_vector(int n)
{
if (0 <= n && n < 6) {
return FixPIMDLangevin::compute_vector(n);
}
return 0.0;
}

50
src/fix_pimdb_langevin.h
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/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(pimdb/langevin,FixPIMDBLangevin);
#else
#ifndef FIX_PIMDB_LANGEVIN_H
#define FIX_PIMDB_LANGEVIN_H
#include "fix_pimd_langevin.h"
#include "bosonic_exchange.h"
namespace LAMMPS_NS {
class FixPIMDBLangevin : public FixPIMDLangevin {
public:
FixPIMDBLangevin(class LAMMPS *, int, char **);
~FixPIMDBLangevin();
double compute_vector(int) override;
void compute_spring_energy() override;
void compute_t_prim() override;
protected:
void spring_force() override;
private:
int nbosons;
BosonicExchange bosonic_exchange;
double** f_tag_order;
};
}
#endif
#endif

124
src/fix_pimdb_nvt.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Package FixPIMDNVT
Purpose Quantum Path Integral Algorithm for Quantum Chemistry
Copyright Voth Group @ University of Chicago
Authors Chris Knight & Yuxing Peng (yuxing at uchicago.edu)
Updated Oct-01-2011
Version 1.0
------------------------------------------------------------------------- */
#include "fix_pimdb_nvt.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "math_const.h"
#include "math_special.h"
#include "memory.h"
#include "universe.h"
#include "update.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
using MathSpecial::powint;
enum{PIMD,NMPIMD,CMD};
/* ---------------------------------------------------------------------- */
FixPIMDBNVT::FixPIMDBNVT(LAMMPS *lmp, int narg, char **arg) :
FixPIMDNVT(lmp, narg, arg),
bosonic_exchange(lmp, atom->nlocal, np, universe->me,false)
{
beta = 1.0 / force->boltz / nhc_temp;
virial = 0.;
prim = 0.;
spring_energy = 0.;
size_vector = 4;
if (method != PIMD && method != NMPIMD) {
error->universe_all(FLERR, "Method not supported in fix pimdb/nvt; only methods PIMD and NMPIMD");
}
}
/* ---------------------------------------------------------------------- */
FixPIMDBNVT::~FixPIMDBNVT() {
}
void FixPIMDBNVT::post_force(int /*flag*/)
{
double **x = atom->x;
double **f = atom->f;
for (int i = 0; i < atom->nlocal; i++)
for (int j = 0; j < 3; j++) atom->f[i][j] /= np;
comm_exec(atom->x);
virial = bosonic_exchange.vir_estimator(x, f);
if (0 == universe->me)
{
prim = bosonic_exchange.prim_estimator();
spring_energy = bosonic_exchange.get_potential();
}
else {
prim = -bosonic_exchange.get_spring_energy();
spring_energy = bosonic_exchange.get_spring_energy();
}
spring_force(x, f);
if (method == NMPIMD)
{
/* forward comm for the force on ghost atoms */
nmpimd_fill(atom->f);
/* inter-partition comm */
comm_exec(atom->f);
/* normal-mode transform */
nmpimd_transform(buf_beads, atom->f, M_f2fp[universe->iworld]);
}
}
/* ---------------------------------------------------------------------- */
void FixPIMDBNVT::spring_force(double **x, double **f)
{
double *xlast = buf_beads[x_last];
double *xnext = buf_beads[x_next];
double ff = fbond * atom->mass[atom->type[0]];
bosonic_exchange.prepare_with_coordinates(*x, xlast, xnext, beta, 1 / beta, -ff);
bosonic_exchange.spring_force(f);
}
/* ---------------------------------------------------------------------- */
double FixPIMDBNVT::compute_vector(int n)
{
if (n == 0) return spring_energy;
if (n == 1) return t_sys;
if (n == 2) return virial;
if (n == 3) return prim;
return 0.0;
}

50
src/fix_pimdb_nvt.h
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/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
// clang-format off
FixStyle(pimdb/nvt,FixPIMDBNVT);
// clang-format on
#else
#ifndef FIX_PIMDB_NVT_H
#define FIX_PIMDB_NVT_H
#include "fix_pimd_nvt.h"
#include "bosonic_exchange.h"
namespace LAMMPS_NS {
class FixPIMDBNVT : public FixPIMDNVT {
public:
FixPIMDBNVT(class LAMMPS *, int, char **);
~FixPIMDBNVT();
void post_force(int) override;
double compute_vector(int) override;
protected:
void spring_force(double **x, double **f);
void vir_estimator(double **x, double **f);
BosonicExchange bosonic_exchange;
double beta;
double virial;
double prim;
double spring_energy;
};
} // namespace LAMMPS_NS
#endif
#endif