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This commit is contained in:
Axel Kohlmeyer
2023-02-24 15:41:04 -05:00
parent c5f29dee39
commit ed822f8002
6 changed files with 361 additions and 0 deletions
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62
examples/PACKAGES/alchemy/h2o.mol Normal file
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# Water molecule. SPC/E model.
3 atoms
2 bonds
1 angles
Coords
1 1.12456 0.09298 1.27452
2 1.53683 0.75606 1.89928
3 0.49482 0.56390 0.65678
Types
1 1
2 2
3 2
Charges
1 -0.8472
2 0.4236
3 0.4236
Bonds
1 1 1 2
2 1 1 3
Angles
1 1 2 1 3
Shake Flags
1 1
2 1
3 1
Shake Atoms
1 1 2 3
2 1 2 3
3 1 2 3
Shake Bond Types
1 1 1 1
2 1 1 1
3 1 1 1
Special Bond Counts
1 2 0 0
2 1 1 0
3 1 1 0
Special Bonds
1 2 3
2 1 3
3 1 2

39
examples/PACKAGES/alchemy/h3o+.mol Normal file
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# Hydronium ion. SPC/E model.
4 atoms
3 bonds
3 angles
Coords
1 0.00000 1.00000 0.00000
2 0.00000 0.00000 0.00000
3 0.00000 -0.50000 -0.8660
4 0.00000 -0.50000 0.8660
Types
1 2
2 1
3 2
4 2
Charges
1 0.56775
2 -0.70305
3 0.56775
4 0.56775
Bonds
1 1 2 1
2 1 2 3
3 1 2 4
Angles
1 1 1 2 3
1 1 3 2 4
1 1 1 2 4

53
examples/PACKAGES/alchemy/in.twowater Normal file
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# set up names for two partitions with different topologies
variable name world twowater twoions
units real
atom_style full
atom_modify map array
region box block -10 10 -10 10 -10 10
boundary m m m
create_box 2 box bond/types 1 angle/types 1 &
extra/bond/per/atom 3 extra/angle/per/atom 3 extra/special/per/atom 3
mass 1 15.9994
mass 2 1.008
pair_style lj/cut/coul/cut 10.0
pair_coeff 1 1 0.1553 3.166
pair_coeff 1 2 0.0 1.0
pair_coeff 2 2 0.0 1.0
bond_style harmonic
bond_coeff 1 1000.0 1.0
angle_style harmonic
angle_coeff 1 100.0 109.47
molecule water h2o.mol
molecule hydronium h3o+.mol
molecule hydroxyl oh-.mol
timestep 0.1
# generate different topologies with the same number of atoms
if "${name} == twowater" then &
"create_atoms 0 single -2.0 0.0 0.0 mol water 453624" &
"create_atoms 0 single 2.0 0.0 0.0 mol water 767353" &
else &
"create_atoms 0 single 2.0 0.0 0.0 mol hydroxyl 767353" &
"create_atoms 0 single -2.0 0.0 0.0 mol hydronium 453624"
velocity all create 100 5463576
fix 1 all nve
fix 2 all alchemy
dump 1 all atom 100 ${name}.lammpstrj
dump_modify 1 sort id
thermo_style custom step temp press etotal pe ke f_2[*]
thermo 100
reset_timestep 100
run 10000 start 0 stop 20000

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examples/PACKAGES/alchemy/oh-.mol Normal file
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# Hydroxyl ion. SPC/E model.
2 atoms
1 bonds
Coords
1 0.5 0.0 0.0
2 -0.5 0.0 0.0
Types
1 1
2 2
Charges
1 -1.1354
2 0.1354
Bonds
1 1 1 2

134
src/REPLICA/fix_alchemy.cpp Normal file
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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.
------------------------------------------------------------------------- */
#include "fix_alchemy.h"
#include "atom.h"
#include "comm.h"
#include "error.h"
#include "memory.h"
#include "universe.h"
#include "update.h"
using namespace LAMMPS_NS;
using namespace FixConst;
/* ---------------------------------------------------------------------- */
static double get_lambda(const bigint &step, const bigint &begin, const bigint &end, int iworld)
{
double lambda = step - begin;
if (lambda != 0.0) lambda /= end - begin;
if (iworld == 0) lambda = 1.0 - lambda;
return lambda;
}
/* ---------------------------------------------------------------------- */
FixAlchemy::FixAlchemy(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), coordbuf(nullptr)
{
lambda = epot[0] = epot[1] = 0.0;
no_change_box = 1;
vector_flag = 1;
size_vector = 3;
extvector = 0;
// set up communicators
if (universe->nworlds != 2) error->all(FLERR, "Must use exactly two partitions");
int color = comm->me;
int key = universe->iworld;
MPI_Comm_split(universe->uworld, color, key, &samerank);
if (narg != 3) error->all(FLERR, "Incorrect number of arguments for fix alchemy");
}
/* ---------------------------------------------------------------------- */
FixAlchemy::~FixAlchemy()
{
MPI_Comm_free(&samerank);
}
/* ---------------------------------------------------------------------- */
int FixAlchemy::setmask()
{
int mask = 0;
mask |= POST_INTEGRATE;
mask |= POST_FORCE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixAlchemy::init() {}
/* ---------------------------------------------------------------------- */
void FixAlchemy::setup(int /*vflag*/)
{
const int nall = atom->nlocal;
const auto tag = atom->tag;
const auto x = atom->x;
memory->destroy(coordbuf);
memory->create(coordbuf, 4 * sizeof(double) * nall, "alchemy:coordbuf");
if (universe->iworld == 0) {
int m = 0;
for (int i = 0; i < nall; ++i) {
coordbuf[m++] = ubuf(tag[i]).d;
coordbuf[m++] = x[i][0];
coordbuf[m++] = x[i][1];
coordbuf[m++] = x[i][2];
}
}
MPI_Bcast(coordbuf, 4 * nall, MPI_DOUBLE, 0, samerank);
if (universe->iworld == 1) {
int m = 0;
for (int i = 0; i < nall; ++i) {
tagint mytag = (tagint) ubuf(coordbuf[m++]).i;
x[atom->map(mytag)][0] = coordbuf[m++];
x[atom->map(mytag)][1] = coordbuf[m++];
x[atom->map(mytag)][2] = coordbuf[m++];
}
}
lambda = get_lambda(update->ntimestep, update->beginstep, update->endstep, universe->iworld);
}
/* ---------------------------------------------------------------------- */
void FixAlchemy::post_integrate()
{
int nall = 3 * (atom->nlocal + atom->nghost);
// MPI_Bcast(&atom->x[0][0], nall, MPI_DOUBLE, 0, samerank);
}
/* ---------------------------------------------------------------------- */
void FixAlchemy::post_force(int /*vflag*/)
{
lambda = get_lambda(update->ntimestep, update->beginstep, update->endstep, universe->iworld);
}
/* ---------------------------------------------------------------------- */
double FixAlchemy::compute_vector(int n)
{
if (n == 0) return lambda;
return epot[n - 1];
}

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src/REPLICA/fix_alchemy.h Normal file
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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(alchemy,FixAlchemy);
// clang-format on
#else
#ifndef LMP_FIX_ALCHEMY_H
#define LMP_FIX_ALCHEMY_H
#include "fix.h"
namespace LAMMPS_NS {
class FixAlchemy : public Fix {
public:
FixAlchemy(class LAMMPS *, int, char **);
~FixAlchemy() override;
int setmask() override;
void init() override;
void setup(int) override;
void post_integrate() override;
void post_force(int) override;
double compute_vector(int) override;
protected:
MPI_Comm samerank;
MPI_Comm rankzero;
double *coordbuf;
double lambda; // changes from 0 to 1 during run
double epot[2]; // last (unscaled) potential energy from each replica
};
} // namespace LAMMPS_NS
#endif
#endif