ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

created vashishta/table variant

Browse Source
This commit is contained in:
Steve Plimpton
2016-09-07 11:56:38 -06:00
parent b12ad2cecf
commit 43b05a60c7
7 changed files with 547 additions and 272 deletions
Download Patch File Download Diff File Expand all files Collapse all files

167
doc/src/pair_vashishta.txt
View File

@ -8,26 +8,36 @@
pair_style vashishta command :h3
pair_style vashishta/omp command :h3
pair_style vashishta/table command :h3
[Syntax:]
pair_style vashishta :pre
pair_style style args :pre
style = {vashishta} or {vashishta/table}
args = list of arguments for a particular style :ul
{vashishta} args = none
{vashishta/table} args = Ntable cutinner
Ntable = # of tabulation points
cutinner = tablulate from cutinner to cutoff :pre
[Examples:]
pair_style vashishta
pair_coeff * * SiC.vashishta Si C :pre
pair_style vashishta/table 100000 0.2
pair_coeff * * SiC.vashishta Si C :pre
[Description:]
The {vashishta} style computes the combined 2-body and 3-body
family of potentials developed in the group of Vashishta and
co-workers. By combining repulsive, screened Coulombic,
screened charge-dipole, and dispersion interactions with a
bond-angle energy based on the Stillinger-Weber potential,
this potential has been used to describe a variety of inorganic
compounds, including SiO2 "Vashishta1990"_#Vashishta1990,
SiC "Vashishta2007"_#Vashishta2007,
The {vashishta} and {vashishta/table} styles compute the combined
2-body and 3-body family of potentials developed in the group of
Vashishta and co-workers. By combining repulsive, screened Coulombic,
screened charge-dipole, and dispersion interactions with a bond-angle
energy based on the Stillinger-Weber potential, this potential has
been used to describe a variety of inorganic compounds, including SiO2
"Vashishta1990"_#Vashishta1990, SiC "Vashishta2007"_#Vashishta2007,
and InP "Branicio2009"_#Branicio2009.
The potential for the energy U of a system of atoms is
@ -43,10 +53,19 @@ both zero at {rc}. The summation over three-body terms
is over all neighbors J and K within a cut-off distance = {r0},
where the exponential screening function becomes zero.
Only a single pair_coeff command is used with the {vashishta} style which
specifies a Vashishta potential file with parameters for all
needed elements. These are mapped to LAMMPS atom types by specifying
N additional arguments after the filename in the pair_coeff command,
The {vashishta} style computes these formulas analytically. The
{vashishta/table} style tabulates the analytic values for {Ntable}
points from cutinner to the cutoff of the potential. The points are
equally spaced in R^2 space from cutinner^2 to cutoff^2. For the
two-body term in the above equation, a linear interpolation for each
pairwise distance between adjacent points in the table. In practice
the tabulated version can run 3-5x faster than the analytic version
with little loss of accuracy for Ntable = ???.
Only a single pair_coeff command is used with either style which
specifies a Vashishta potential file with parameters for all needed
elements. These are mapped to LAMMPS atom types by specifying N
additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:
filename
@ -95,59 +114,52 @@ r0 (distance units)
C
costheta0 :ul
The non-annotated parameters are unitless.
The Vashishta potential file must contain entries for all the
elements listed in the pair_coeff command. It can also contain
entries for additional elements not being used in a particular
simulation; LAMMPS ignores those entries.
For a single-element simulation, only a single entry is required
(e.g. SiSiSi). For a two-element simulation, the file must contain 8
entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that
specify parameters for all permutations of the two elements
interacting in three-body configurations. Thus for 3 elements, 27
entries would be required, etc.
The non-annotated parameters are unitless. The Vashishta potential
file must contain entries for all the elements listed in the
pair_coeff command. It can also contain entries for additional
elements not being used in a particular simulation; LAMMPS ignores
those entries. For a single-element simulation, only a single entry
is required (e.g. SiSiSi). For a two-element simulation, the file
must contain 8 entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC,
CCSi, CCC), that specify parameters for all permutations of the two
elements interacting in three-body configurations. Thus for 3
elements, 27 entries would be required, etc.
Depending on the particular version of the Vashishta potential,
the values of these parameters may be keyed to the identities of
zero, one, two, or three elements.
In order to make the input file format unambiguous, general,
and simple to code,
LAMMPS uses a slightly confusing method for specifying parameters.
All parameters are divided into two classes: two-body and three-body.
Two-body and three-body parameters are handled differently,
as described below.
The two-body parameters are H, eta, lambda1, D, lambda4, W, rc, gamma, and r0.
They appear in the above formulae with two subscripts.
The parameters Zi and Zj are also classified as two-body parameters,
even though they only have 1 subscript.
The three-body parameters are B, C, costheta0.
They appear in the above formulae with three subscripts.
Two-body and three-body parameters are handled differently,
as described below.
Depending on the particular version of the Vashishta potential, the
values of these parameters may be keyed to the identities of zero,
one, two, or three elements. In order to make the input file format
unambiguous, general, and simple to code, LAMMPS uses a slightly
confusing method for specifying parameters. All parameters are
divided into two classes: two-body and three-body. Two-body and
three-body parameters are handled differently, as described below.
The two-body parameters are H, eta, lambda1, D, lambda4, W, rc, gamma,
and r0. They appear in the above formulae with two subscripts. The
parameters Zi and Zj are also classified as two-body parameters, even
though they only have 1 subscript. The three-body parameters are B,
C, costheta0. They appear in the above formulae with three
subscripts. Two-body and three-body parameters are handled
differently, as described below.
The first element in each entry is the center atom
in a three-body interaction, while the second and third elements
are two neighbor atoms. Three-body parameters for a central atom I
and two neighbors J and K are taken from the IJK entry.
Note that even though three-body parameters do not depend on the order of
J and K, LAMMPS stores three-body parameters for both IJK and IKJ.
The user must ensure that these values are equal.
Two-body parameters for an atom I interacting with atom J are taken from
the IJJ entry, where the 2nd and 3rd
elements are the same. Thus the two-body parameters
for Si interacting with C come from the SiCC entry. Note that even
though two-body parameters (except possibly gamma and r0 in U3)
do not depend on the order of the two elements,
LAMMPS will get the Si-C value from the SiCC entry
and the C-Si value from the CSiSi entry. The user must ensure
that these values are equal. Two-body parameters appearing
in entries where the 2nd and 3rd elements are different are
stored but never used. It is good practice to enter zero for
these values. Note that the three-body function U3 above
contains the two-body parameters gamma and r0. So U3 for a
central C atom bonded to an Si atom and a second C atom
will take three-body parameters from the CSiC entry, but
two-body parameters from the CCC and CSiSi entries.
The first element in each entry is the center atom in a three-body
interaction, while the second and third elements are two neighbor
atoms. Three-body parameters for a central atom I and two neighbors J
and K are taken from the IJK entry. Note that even though three-body
parameters do not depend on the order of J and K, LAMMPS stores
three-body parameters for both IJK and IKJ. The user must ensure that
these values are equal. Two-body parameters for an atom I interacting
with atom J are taken from the IJJ entry, where the 2nd and 3rd
elements are the same. Thus the two-body parameters for Si interacting
with C come from the SiCC entry. Note that even though two-body
parameters (except possibly gamma and r0 in U3) do not depend on the
order of the two elements, LAMMPS will get the Si-C value from the
SiCC entry and the C-Si value from the CSiSi entry. The user must
ensure that these values are equal. Two-body parameters appearing in
entries where the 2nd and 3rd elements are different are stored but
never used. It is good practice to enter zero for these values. Note
that the three-body function U3 above contains the two-body parameters
gamma and r0. So U3 for a central C atom bonded to an Si atom and a
second C atom will take three-body parameters from the CSiC entry, but
two-body parameters from the CCC and CSiSi entries.
:line
@ -181,13 +193,7 @@ two different element types, mixing is performed by LAMMPS as
described above from values in the potential file.
This pair style does not support the "pair_modify"_pair_modify.html
{shift} and {tail} options, but it supports the {table} option.
Turning on the {table} option will use a linear interpolation table
for force and energy of the two-body term with {2**N} entries.
Tabulation can reduce the computational cost by a factor of 2-3
with 20-bit to 12-bit table sizes, respectively, at a small to
moderate reduction in precision. It is not recommended to use
smaller than 12-bit tables.
shift, table, and tail options.
This pair style does not write its information to "binary restart
files"_restart.html, since it is stored in potential files. Thus, you
@ -209,11 +215,11 @@ the "Making LAMMPS"_Section_start.html#start_3 section for more info.
This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.
The Vashishta potential files provided with LAMMPS (see the
potentials directory) are parameterized for metal "units"_units.html.
You can use the Vashishta potential with any LAMMPS units, but you would need
to create your own Vashishta potential file with coefficients listed in the
appropriate units if your simulation doesn't use "metal" units.
The Vashishta potential files provided with LAMMPS (see the potentials
directory) are parameterized for metal "units"_units.html. You can
use the Vashishta potential with any LAMMPS units, but you would need
to create your own Vashishta potential file with coefficients listed
in the appropriate units if your simulation doesn't use "metal" units.
[Related commands:]
@ -224,11 +230,14 @@ appropriate units if your simulation doesn't use "metal" units.
:line
:link(Vashishta1990)
[(Vashishta1990)] P. Vashishta, R. K. Kalia, J. P. Rino, Phys. Rev. B 41, 12197 (1990).
[(Vashishta1990)] P. Vashishta, R. K. Kalia, J. P. Rino, Phys. Rev. B
41, 12197 (1990).
:link(Vashishta2007)
[(Vashishta2007)] P. Vashishta, R. K. Kalia, A. Nakano, J. P. Rino. J. Appl. Phys. 101, 103515 (2007).
[(Vashishta2007)] P. Vashishta, R. K. Kalia, A. Nakano,
J. P. Rino. J. Appl. Phys. 101, 103515 (2007).
:link(Branicio2009)
[(Branicio2009)] Branicio, Rino, Gan and Tsuzuki, J. Phys Condensed Matter 21 (2009) 095002
[(Branicio2009)] Branicio, Rino, Gan and Tsuzuki, J. Phys Condensed
Matter 21 (2009) 095002

3
examples/vashishta/in.indiumphosphide-tabulated → examples/vashishta/in.indiumphosphide.table
View File

@ -42,9 +42,8 @@ mass 2 30.98
# choose potential
pair_style vashishta
pair_style vashishta/table 100000 0.2
pair_coeff * * InP.vashishta In P
pair_modify table 16
# setup neighbor style

3
examples/vashishta/in.sio2-tabulated → examples/vashishta/in.sio2.table
View File

@ -11,9 +11,8 @@ replicate 4 4 4
velocity all create 2000.0 277387 mom yes
displace_atoms all move 0.05 0.9 0.4 units box
pair_style vashishta
pair_style vashishta/table 100000 0.2
pair_coeff * * SiO.1990.vashishta Si O
pair_modify table 16
neighbor 0.3 bin
neigh_modify delay 10

196
src/MANYBODY/pair_vashishta.cpp
View File

@ -14,7 +14,6 @@
/* ----------------------------------------------------------------------
Contributing author: Yongnan Xiong (HNU), xyn@hnu.edu.cn
Aidan Thompson (SNL)
Anders Hafreager (UiO), andershaf@gmail.com
------------------------------------------------------------------------- */
#include <math.h>
@ -32,6 +31,7 @@
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MAXLINE 1024
@ -52,15 +52,6 @@ PairVashishta::PairVashishta(LAMMPS *lmp) : Pair(lmp)
params = NULL;
elem2param = NULL;
map = NULL;
neigh3BodyMax = 0;
neigh3BodyCount = NULL;
neigh3Body = NULL;
useTable = false;
nTablebits = 12;
forceTable = NULL;
potentialTable = NULL;
}
/* ----------------------------------------------------------------------
@ -75,11 +66,6 @@ PairVashishta::~PairVashishta()
memory->destroy(params);
memory->destroy(elem2param);
memory->destroy(forceTable);
memory->destroy(potentialTable);
memory->destroy(neigh3BodyCount);
memory->destroy(neigh3Body);
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
@ -87,86 +73,10 @@ PairVashishta::~PairVashishta()
}
}
void PairVashishta::modify_params(int narg, char **arg)
{
if (narg == 0) error->all(FLERR,"Illegal pair_modify command");
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"table") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal pair_modify command");
nTablebits = force->inumeric(FLERR,arg[iarg+1]);
if ((nTablebits < 0) || (nTablebits > sizeof(int)*CHAR_BIT-1))
error->all(FLERR,"Illegal interpolation table size");
if (nTablebits == 0) {
useTable = false;
} else {
useTable = true;
}
iarg += 2;
} else if (strcmp(arg[iarg],"tabinner") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal pair_modify command");
tabinner = force->numeric(FLERR,arg[iarg+1]);
if (tabinner <= 0.0)
error->all(FLERR,"Illegal inner cutoff for tabulation");
iarg += 2;
}
}
updateTables();
}
void PairVashishta::validateNeigh3Body() {
if (atom->nlocal > neigh3BodyMax) {
neigh3BodyMax = atom->nmax;
memory->destroy(neigh3BodyCount);
memory->destroy(neigh3Body);
memory->create(neigh3BodyCount,neigh3BodyMax, "pair:vashishta:neigh3BodyCount");
memory->create(neigh3Body,neigh3BodyMax, 1000, "pair:vashishta:neigh3Body"); // TODO: pick this number more wisely?
}
}
void PairVashishta::updateTables()
{
memory->destroy(forceTable);
memory->destroy(potentialTable);
forceTable = NULL;
potentialTable = NULL;
if (!useTable) return;
int ntable = 1<<nTablebits;
tabinnersq = tabinner*tabinner;
deltaR2 = (cutmax*cutmax - tabinnersq) / (ntable-1);
oneOverDeltaR2 = 1.0/deltaR2;
memory->create(forceTable,nelements,nelements,ntable+1,"pair:vashishta:forceTable");
memory->create(potentialTable,nelements,nelements,ntable+1,"pair:vashishta:potentialTable");
for (int i = 0; i < nelements; i++) {
for (int j = 0; j < nelements; j++) {
int ijparam = elem2param[i][j][j];
for(int idx=0; idx <= ntable; idx++) {
double rsq = tabinnersq + idx*deltaR2;
double fpair, eng;
// call analytical version of two-body term function
twobody(params[ijparam], rsq, fpair, 1, eng, false);
forceTable[i][j][idx] = fpair;
potentialTable[i][j][idx] = eng;
}
}
}
}
/* ---------------------------------------------------------------------- */
void PairVashishta::compute(int eflag, int vflag)
{
validateNeigh3Body();
int i,j,k,ii,jj,kk,inum,jnum,jnumm1;
int itype,jtype,ktype,ijparam,ikparam,ijkparam;
tagint itag,jtag;
@ -201,8 +111,6 @@ void PairVashishta::compute(int eflag, int vflag)
ytmp = x[i][1];
ztmp = x[i][2];
neigh3BodyCount[i] = 0; // Reset the 3-body neighbor list
// two-body interactions, skip half of them
jlist = firstneigh[i];
@ -213,21 +121,6 @@ void PairVashishta::compute(int eflag, int vflag)
j &= NEIGHMASK;
jtag = tag[j];
jtype = map[type[j]];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
ijparam = elem2param[itype][jtype][jtype];
if (rsq <= params[ijparam].cutsq2) {
neigh3Body[i][neigh3BodyCount[i]] = j;
neigh3BodyCount[i]++;
}
if (rsq > params[ijparam].cutsq) continue;
if (itag > jtag) {
if ((itag+jtag) % 2 == 0) continue;
} else if (itag < jtag) {
@ -238,7 +131,17 @@ void PairVashishta::compute(int eflag, int vflag)
if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
}
twobody(params[ijparam],rsq,fpair,eflag,evdwl, useTable);
jtype = map[type[j]];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
ijparam = elem2param[itype][jtype][jtype];
if (rsq > params[ijparam].cutsq) continue;
twobody(&params[ijparam],rsq,fpair,eflag,evdwl);
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
@ -251,8 +154,6 @@ void PairVashishta::compute(int eflag, int vflag)
evdwl,0.0,fpair,delx,dely,delz);
}
jlist = neigh3Body[i];
jnum = neigh3BodyCount[i];
jnumm1 = jnum - 1;
for (jj = 0; jj < jnumm1; jj++) {
@ -635,55 +536,32 @@ void PairVashishta::setup_params()
if (params[m].cut > cutmax) cutmax = params[m].cut;
if (params[m].r0 > cutmax) cutmax = params[m].r0;
}
updateTables();
}
/* ---------------------------------------------------------------------- */
void PairVashishta::twobody(const Param &param, double rsq, double &fforce,
int eflag, double &eng, bool tabulated)
void PairVashishta::twobody(Param *param, double rsq, double &fforce,
int eflag, double &eng)
{
if (tabulated) {
if (rsq < tabinnersq) {
sprintf(estr,"Pair distance < table inner cutoff: "
"ijtype %d %d dist %g",param.ielement+1,param.jelement+1,sqrt(rsq));
error->one(FLERR,estr);
}
double r,rinvsq,r4inv,r6inv,reta,lam1r,lam4r,vc2,vc3;
const int tableIndex = (rsq - tabinnersq)*oneOverDeltaR2;
// double - int will only keep the 0.xxxx part
const double fraction = (rsq - tabinnersq)*oneOverDeltaR2 - tableIndex;
r = sqrt(rsq);
rinvsq = 1.0/rsq;
r4inv = rinvsq*rinvsq;
r6inv = rinvsq*r4inv;
reta = pow(r,-param->eta);
lam1r = r*param->lam1inv;
lam4r = r*param->lam4inv;
vc2 = param->zizj * exp(-lam1r)/r;
vc3 = param->mbigd * r4inv*exp(-lam4r);
double force0 = forceTable[param.ielement][param.jelement][tableIndex];
double force1 = forceTable[param.ielement][param.jelement][tableIndex+1];
fforce = (1.0 - fraction)*force0 + fraction*force1; // force is linearly interpolated between the two values
if (evflag) {
double energy0 = potentialTable[param.ielement][param.jelement][tableIndex];
double energy1 = potentialTable[param.ielement][param.jelement][tableIndex+1];
eng = (1.0 - fraction)*energy0 + fraction*energy1;
}
} else {
double r,rinvsq,r4inv,r6inv,reta,lam1r,lam4r,vc2,vc3;
r = sqrt(rsq);
rinvsq = 1.0/rsq;
r4inv = rinvsq*rinvsq;
r6inv = rinvsq*r4inv;
reta = pow(r,-param.eta);
lam1r = r*param.lam1inv;
lam4r = r*param.lam4inv;
vc2 = param.zizj * exp(-lam1r)/r;
vc3 = param.mbigd * r4inv*exp(-lam4r);
fforce = (param.dvrc*r
- (4.0*vc3 + lam4r*vc3+param.big6w*r6inv
- param.heta*reta - vc2 - lam1r*vc2)
) * rinvsq;
if (eflag) eng = param.bigh*reta
+ vc2 - vc3 - param.bigw*r6inv
- r*param.dvrc + param.c0;
}
fforce = (param->dvrc*r
- (4.0*vc3 + lam4r*vc3+param->big6w*r6inv
- param->heta*reta - vc2 - lam1r*vc2)
) * rinvsq;
if (eflag) eng = param->bigh*reta
+ vc2 - vc3 - param->bigw*r6inv
- r*param->dvrc + param->c0;
}
/* ---------------------------------------------------------------------- */
@ -742,15 +620,3 @@ void PairVashishta::threebody(Param *paramij, Param *paramik, Param *paramijk,
if (eflag) eng = facrad;
}
/* ----------------------------------------------------------------------
* add memory usage for tabulation
* ---------------------------------------------------------------------- */
double PairVashishta::memory_usage()
{
double bytes = Pair::memory_usage();
if (useTable)
bytes += 2*nelements*nelements*sizeof(double)*(1<<nTablebits);
return bytes;
}

32
src/MANYBODY/pair_vashishta.h
View File

@ -17,8 +17,8 @@ PairStyle(vashishta,PairVashishta)
#else
#ifndef LMP_PAIR_Vashishta_H
#define LMP_PAIR_Vashishta_H
#ifndef LMP_PAIR_VASHISHITA_H
#define LMP_PAIR_VASHISHITA_H
#include "pair.h"
@ -28,13 +28,11 @@ class PairVashishta : public Pair {
public:
PairVashishta(class LAMMPS *);
virtual ~PairVashishta();
virtual void modify_params(int, char **);
virtual void compute(int, int);
void settings(int, char **);
virtual void settings(int, char **);
void coeff(int, char **);
virtual double init_one(int, int);
virtual void init_style();
virtual double memory_usage();
double init_one(int, int);
void init_style();
protected:
struct Param {
@ -48,33 +46,19 @@ class PairVashishta : public Pair {
int ielement,jelement,kelement;
};
bool useTable;
int nTablebits;
double deltaR2;
double oneOverDeltaR2;
double ***forceTable; // Table containing the forces
double ***potentialTable; // Table containing the potential energies
int neigh3BodyMax; // Max size of short neighborlist
int *neigh3BodyCount; // Number of neighbors in short range 3 particle forces neighbor list
int **neigh3Body; // Neighborlist for short range 3 particle forces
double cutmax; // max cutoff for all elements
int nelements; // # of unique elements
char **elements; // names of unique elements
int ***elem2param; // mapping from element triplets to parameters
int *map; // mapping from atom types to elements
char estr[128]; // Char array to store error message with sprintf (i.e. twobody table)
int nparams; // # of stored parameter sets
int maxparam; // max # of parameter sets
Param *params; // parameter set for an I-J-K interaction
virtual void allocate();
void allocate();
void read_file(char *);
void setup_params();
void updateTables();
void validateNeigh3Body();
void twobody(const Param &, double, double &, int, double &, bool tabulated=false);
virtual void setup_params();
void twobody(Param *, double, double &, int, double &);
void threebody(Param *, Param *, Param *, double, double, double *, double *,
double *, double *, int, double &);
};

313
src/MANYBODY/pair_vashishta_table.cpp Executable file
View File

@ -0,0 +1,313 @@
/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Anders Hafreager (UiO), andershaf@gmail.com
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_vashishta_table.h"
#include "atom.h"
#include "neighbor.h"
#include "neigh_request.h"
#include "force.h"
#include "comm.h"
#include "memory.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairVashishtaTable::PairVashishtaTable(LAMMPS *lmp) : PairVashishta(lmp)
{
neigh3BodyMax = 0;
neigh3BodyCount = NULL;
neigh3Body = NULL;
forceTable = NULL;
potentialTable = NULL;
}
/* ----------------------------------------------------------------------
check if allocated, since class can be destructed when incomplete
------------------------------------------------------------------------- */
PairVashishtaTable::~PairVashishtaTable()
{
memory->destroy(forceTable);
memory->destroy(potentialTable);
memory->destroy(neigh3BodyCount);
memory->destroy(neigh3Body);
}
/* ---------------------------------------------------------------------- */
void PairVashishtaTable::compute(int eflag, int vflag)
{
int i,j,k,ii,jj,kk,inum,jnum,jnumm1;
int itype,jtype,ktype,ijparam,ikparam,ijkparam;
tagint itag,jtag;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,rsq1,rsq2;
double delr1[3],delr2[3],fj[3],fk[3];
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **f = atom->f;
tagint *tag = atom->tag;
int *type = atom->type;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// reallocate 3-body neighbor list if necessary
// NOTE: using 1000 is inefficient
// could make this a LAMMPS paged neighbor list
if (nlocal > neigh3BodyMax) {
neigh3BodyMax = atom->nmax;
memory->destroy(neigh3BodyCount);
memory->destroy(neigh3Body);
memory->create(neigh3BodyCount,neigh3BodyMax,
"pair:vashishta:neigh3BodyCount");
memory->create(neigh3Body,neigh3BodyMax,1000,
"pair:vashishta:neigh3Body");
}
// loop over full neighbor list of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
itag = tag[i];
itype = map[type[i]];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
// reset the 3-body neighbor list
neigh3BodyCount[i] = 0;
// two-body interactions, skip half of them
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtag = tag[j];
jtype = map[type[j]];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
ijparam = elem2param[itype][jtype][jtype];
if (rsq <= params[ijparam].cutsq2) {
neigh3Body[i][neigh3BodyCount[i]] = j;
neigh3BodyCount[i]++;
}
if (rsq > params[ijparam].cutsq) continue;
if (itag > jtag) {
if ((itag+jtag) % 2 == 0) continue;
} else if (itag < jtag) {
if ((itag+jtag) % 2 == 1) continue;
} else {
if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
}
twobody_table(params[ijparam],rsq,fpair,eflag,evdwl);
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
}
jlist = neigh3Body[i];
jnum = neigh3BodyCount[i];
jnumm1 = jnum - 1;
for (jj = 0; jj < jnumm1; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtype = map[type[j]];
ijparam = elem2param[itype][jtype][jtype];
delr1[0] = x[j][0] - xtmp;
delr1[1] = x[j][1] - ytmp;
delr1[2] = x[j][2] - ztmp;
rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
if (rsq1 >= params[ijparam].cutsq2) continue;
for (kk = jj+1; kk < jnum; kk++) {
k = jlist[kk];
k &= NEIGHMASK;
ktype = map[type[k]];
ikparam = elem2param[itype][ktype][ktype];
ijkparam = elem2param[itype][jtype][ktype];
delr2[0] = x[k][0] - xtmp;
delr2[1] = x[k][1] - ytmp;
delr2[2] = x[k][2] - ztmp;
rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
if (rsq2 >= params[ikparam].cutsq2) continue;
threebody(&params[ijparam],&params[ikparam],&params[ijkparam],
rsq1,rsq2,delr1,delr2,fj,fk,eflag,evdwl);
f[i][0] -= fj[0] + fk[0];
f[i][1] -= fj[1] + fk[1];
f[i][2] -= fj[2] + fk[2];
f[j][0] += fj[0];
f[j][1] += fj[1];
f[j][2] += fj[2];
f[k][0] += fk[0];
f[k][1] += fk[1];
f[k][2] += fk[2];
if (evflag) ev_tally3(i,j,k,evdwl,0.0,fj,fk,delr1,delr2);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ---------------------------------------------------------------------- */
void PairVashishtaTable::twobody_table(const Param &param, double rsq,
double &fforce, int eflag, double &eng)
{
// use analytic form if rsq is inside inner cutoff
if (rsq < tabinnersq) {
Param *pparam = const_cast<Param *> (&param);
PairVashishta::twobody(pparam,rsq,fforce,eflag,eng);
return;
}
// double -> int will only keep the 0.xxxx part
const int tableIndex = (rsq - tabinnersq)*oneOverDeltaR2;
const double fraction = (rsq - tabinnersq)*oneOverDeltaR2 - tableIndex;
// force/energy are linearly interpolated between two adjacent values
double force0 = forceTable[param.ielement][param.jelement][tableIndex];
double force1 = forceTable[param.ielement][param.jelement][tableIndex+1];
fforce = (1.0 - fraction)*force0 + fraction*force1;
if (evflag) {
double energy0 = potentialTable[param.ielement][param.jelement][tableIndex];
double energy1 = potentialTable[param.ielement][param.jelement]
[tableIndex+1];
eng = (1.0 - fraction)*energy0 + fraction*energy1;
}
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairVashishtaTable::settings(int narg, char **arg)
{
if (narg != 2) error->all(FLERR,"Illegal pair_style command");
ntable = force->inumeric(FLERR,arg[0]);
tabinner = force->numeric(FLERR,arg[1]);
if (tabinner <= 0.0)
error->all(FLERR,"Illegal inner cutoff for tabulation");
}
/* ---------------------------------------------------------------------- */
void PairVashishtaTable::setup_params()
{
PairVashishta::setup_params();
create_tables();
}
/* ---------------------------------------------------------------------- */
void PairVashishtaTable::create_tables()
{
memory->destroy(forceTable);
memory->destroy(potentialTable);
forceTable = NULL;
potentialTable = NULL;
tabinnersq = tabinner*tabinner;
deltaR2 = (cutmax*cutmax - tabinnersq) / (ntable-1);
oneOverDeltaR2 = 1.0/deltaR2;
memory->create(forceTable,nelements,nelements,ntable+1,
"pair:vashishta:forceTable");
memory->create(potentialTable,nelements,nelements,ntable+1,
"pair:vashishta:potentialTable");
// tabulalate energy/force via analytic twobody() in parent
int i,j,idx;
double rsq,fpair,eng;
for (i = 0; i < nelements; i++) {
for (j = 0; j < nelements; j++) {
int ijparam = elem2param[i][j][j];
for (idx = 0; idx <= ntable; idx++) {
rsq = tabinnersq + idx*deltaR2;
PairVashishta::twobody(&params[ijparam],rsq,fpair,1,eng);
forceTable[i][j][idx] = fpair;
potentialTable[i][j][idx] = eng;
}
}
}
}
/* ----------------------------------------------------------------------
memory usage of tabulation arrays
------------------------------------------------------------------------- */
double PairVashishtaTable::memory_usage()
{
double bytes = 2*nelements*nelements*sizeof(double)*ntable;
return bytes;
}

105
src/MANYBODY/pair_vashishta_table.h Executable file
View File

@ -0,0 +1,105 @@
/* ----------------------------------------------------------------------
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 PAIR_CLASS
PairStyle(vashishta/table,PairVashishtaTable)
#else
#ifndef LMP_PAIR_VASHISHITA_TABLE_H
#define LMP_PAIR_VASHISHITA_TABLE_H
#include "pair_vashishta.h"
namespace LAMMPS_NS {
class PairVashishtaTable : public PairVashishta {
public:
PairVashishtaTable(class LAMMPS *);
~PairVashishtaTable();
void compute(int, int);
void settings(int, char **);
double memory_usage();
private:
int ntable;
double deltaR2;
double oneOverDeltaR2;
double ***forceTable; // table of forces per element pair
double ***potentialTable; // table of potential energies
int neigh3BodyMax; // max size of short neighborlist
int *neigh3BodyCount; // # of neighbors in short range
// 3 particle forces neighbor list
int **neigh3Body; // neighlist for short range 3 particle forces
void twobody_table(const Param &, double, double &, int, double &);
void setup_params();
void create_tables();
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.
E: Pair style Vashishta requires atom IDs
This is a requirement to use the Vashishta potential.
E: Pair style Vashishta requires newton pair on
See the newton command. This is a restriction to use the Vashishta
potential.
E: All pair coeffs are not set
All pair coefficients must be set in the data file or by the
pair_coeff command before running a simulation.
E: Cannot open Vashishta potential file %s
The specified Vashishta potential file cannot be opened. Check that the path
and name are correct.
E: Incorrect format in Vashishta potential file
Incorrect number of words per line in the potential file.
E: Illegal Vashishta parameter
One or more of the coefficients defined in the potential file is
invalid.
E: Potential file has duplicate entry
The potential file has more than one entry for the same element.
E: Potential file is missing an entry
The potential file does not have a needed entry.
*/