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created vashishta/table variant

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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
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167
doc/src/pair_vashishta.txt
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@ -8,26 +8,36 @@
pair_style vashishta command :h3 pair_style vashishta command :h3
pair_style vashishta/omp command :h3 pair_style vashishta/omp command :h3
pair_style vashishta/table command :h3
[Syntax:] [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:] [Examples:]
pair_style vashishta pair_style vashishta
pair_coeff * * SiC.vashishta Si C :pre pair_coeff * * SiC.vashishta Si C :pre
pair_style vashishta/table 100000 0.2
pair_coeff * * SiC.vashishta Si C :pre
[Description:] [Description:]
The {vashishta} style computes the combined 2-body and 3-body The {vashishta} and {vashishta/table} styles compute the combined
family of potentials developed in the group of Vashishta and 2-body and 3-body family of potentials developed in the group of
co-workers. By combining repulsive, screened Coulombic, Vashishta and co-workers. By combining repulsive, screened Coulombic,
screened charge-dipole, and dispersion interactions with a screened charge-dipole, and dispersion interactions with a bond-angle
bond-angle energy based on the Stillinger-Weber potential, energy based on the Stillinger-Weber potential, this potential has
this potential has been used to describe a variety of inorganic been used to describe a variety of inorganic compounds, including SiO2
compounds, including SiO2 "Vashishta1990"_#Vashishta1990, "Vashishta1990"_#Vashishta1990, SiC "Vashishta2007"_#Vashishta2007,
SiC "Vashishta2007"_#Vashishta2007,
and InP "Branicio2009"_#Branicio2009. and InP "Branicio2009"_#Branicio2009.
The potential for the energy U of a system of atoms is 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}, is over all neighbors J and K within a cut-off distance = {r0},
where the exponential screening function becomes zero. where the exponential screening function becomes zero.
Only a single pair_coeff command is used with the {vashishta} style which The {vashishta} style computes these formulas analytically. The
specifies a Vashishta potential file with parameters for all {vashishta/table} style tabulates the analytic values for {Ntable}
needed elements. These are mapped to LAMMPS atom types by specifying points from cutinner to the cutoff of the potential. The points are
N additional arguments after the filename in the pair_coeff command, 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: where N is the number of LAMMPS atom types:
filename filename
@ -95,59 +114,52 @@ r0 (distance units)
C C
costheta0 :ul costheta0 :ul
The non-annotated parameters are unitless. The non-annotated parameters are unitless. The Vashishta potential
The Vashishta potential file must contain entries for all the file must contain entries for all the elements listed in the
elements listed in the pair_coeff command. It can also contain pair_coeff command. It can also contain entries for additional
entries for additional elements not being used in a particular elements not being used in a particular simulation; LAMMPS ignores
simulation; LAMMPS ignores those entries. those entries. For a single-element simulation, only a single entry
For a single-element simulation, only a single entry is required is required (e.g. SiSiSi). For a two-element simulation, the file
(e.g. SiSiSi). For a two-element simulation, the file must contain 8 must contain 8 entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC,
entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that CCSi, CCC), that specify parameters for all permutations of the two
specify parameters for all permutations of the two elements elements interacting in three-body configurations. Thus for 3
interacting in three-body configurations. Thus for 3 elements, 27 elements, 27 entries would be required, etc.
entries would be required, etc.
Depending on the particular version of the Vashishta potential, Depending on the particular version of the Vashishta potential, the
the values of these parameters may be keyed to the identities of values of these parameters may be keyed to the identities of zero,
zero, one, two, or three elements. one, two, or three elements. In order to make the input file format
In order to make the input file format unambiguous, general, unambiguous, general, and simple to code, LAMMPS uses a slightly
and simple to code, confusing method for specifying parameters. All parameters are
LAMMPS uses a slightly confusing method for specifying parameters. divided into two classes: two-body and three-body. Two-body and
All parameters are divided into two classes: two-body and three-body. three-body parameters are handled differently, as described below.
Two-body and three-body parameters are handled differently, The two-body parameters are H, eta, lambda1, D, lambda4, W, rc, gamma,
as described below. and r0. They appear in the above formulae with two subscripts. The
The two-body parameters are H, eta, lambda1, D, lambda4, W, rc, gamma, and r0. parameters Zi and Zj are also classified as two-body parameters, even
They appear in the above formulae with two subscripts. though they only have 1 subscript. The three-body parameters are B,
The parameters Zi and Zj are also classified as two-body parameters, C, costheta0. They appear in the above formulae with three
even though they only have 1 subscript. subscripts. Two-body and three-body parameters are handled
The three-body parameters are B, C, costheta0. differently, as described below.
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 The first element in each entry is the center atom in a three-body
in a three-body interaction, while the second and third elements interaction, while the second and third elements are two neighbor
are two neighbor atoms. Three-body parameters for a central atom I atoms. Three-body parameters for a central atom I and two neighbors J
and two neighbors J and K are taken from the IJK entry. and K are taken from the IJK entry. Note that even though three-body
Note that even though three-body parameters do not depend on the order of parameters do not depend on the order of J and K, LAMMPS stores
J and K, LAMMPS stores three-body parameters for both IJK and IKJ. three-body parameters for both IJK and IKJ. The user must ensure that
The user must ensure that these values are equal. these values are equal. Two-body parameters for an atom I interacting
Two-body parameters for an atom I interacting with atom J are taken from with atom J are taken from the IJJ entry, where the 2nd and 3rd
the IJJ entry, where the 2nd and 3rd elements are the same. Thus the two-body parameters for Si interacting
elements are the same. Thus the two-body parameters with C come from the SiCC entry. Note that even though two-body
for Si interacting with C come from the SiCC entry. Note that even parameters (except possibly gamma and r0 in U3) do not depend on the
though two-body parameters (except possibly gamma and r0 in U3) order of the two elements, LAMMPS will get the Si-C value from the
do not depend on the order of the two elements, SiCC entry and the C-Si value from the CSiSi entry. The user must
LAMMPS will get the Si-C value from the SiCC entry ensure that these values are equal. Two-body parameters appearing in
and the C-Si value from the CSiSi entry. The user must ensure entries where the 2nd and 3rd elements are different are stored but
that these values are equal. Two-body parameters appearing never used. It is good practice to enter zero for these values. Note
in entries where the 2nd and 3rd elements are different are that the three-body function U3 above contains the two-body parameters
stored but never used. It is good practice to enter zero for gamma and r0. So U3 for a central C atom bonded to an Si atom and a
these values. Note that the three-body function U3 above second C atom will take three-body parameters from the CSiC entry, but
contains the two-body parameters gamma and r0. So U3 for a two-body parameters from the CCC and CSiSi entries.
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 :line
@ -181,13 +193,7 @@ two different element types, mixing is performed by LAMMPS as
described above from values in the potential file. described above from values in the potential file.
This pair style does not support the "pair_modify"_pair_modify.html This pair style does not support the "pair_modify"_pair_modify.html
{shift} and {tail} options, but it supports the {table} option. shift, table, and tail options.
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.
This pair style does not write its information to "binary restart This pair style does not write its information to "binary restart
files"_restart.html, since it is stored in potential files. Thus, you 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" This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions. for pair interactions.
The Vashishta potential files provided with LAMMPS (see the The Vashishta potential files provided with LAMMPS (see the potentials
potentials directory) are parameterized for metal "units"_units.html. directory) are parameterized for metal "units"_units.html. You can
You can use the Vashishta potential with any LAMMPS units, but you would need use the Vashishta potential with any LAMMPS units, but you would need
to create your own Vashishta potential file with coefficients listed in the to create your own Vashishta potential file with coefficients listed
appropriate units if your simulation doesn't use "metal" units. in the appropriate units if your simulation doesn't use "metal" units.
[Related commands:] [Related commands:]
@ -224,11 +230,14 @@ appropriate units if your simulation doesn't use "metal" units.
:line :line
:link(Vashishta1990) :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) :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) :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
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@ -42,9 +42,8 @@ mass 2 30.98
# choose potential # choose potential
pair_style vashishta pair_style vashishta/table 100000 0.2
pair_coeff * * InP.vashishta In P pair_coeff * * InP.vashishta In P
pair_modify table 16
# setup neighbor style # 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 velocity all create 2000.0 277387 mom yes
displace_atoms all move 0.05 0.9 0.4 units box 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_coeff * * SiO.1990.vashishta Si O
pair_modify table 16
neighbor 0.3 bin neighbor 0.3 bin
neigh_modify delay 10 neigh_modify delay 10

196
src/MANYBODY/pair_vashishta.cpp
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@ -14,7 +14,6 @@
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
Contributing author: Yongnan Xiong (HNU), xyn@hnu.edu.cn Contributing author: Yongnan Xiong (HNU), xyn@hnu.edu.cn
Aidan Thompson (SNL) Aidan Thompson (SNL)
Anders Hafreager (UiO), andershaf@gmail.com
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <math.h> #include <math.h>
@ -32,6 +31,7 @@
#include "neigh_list.h" #include "neigh_list.h"
#include "memory.h" #include "memory.h"
#include "error.h" #include "error.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
#define MAXLINE 1024 #define MAXLINE 1024
@ -52,15 +52,6 @@ PairVashishta::PairVashishta(LAMMPS *lmp) : Pair(lmp)
params = NULL; params = NULL;
elem2param = NULL; elem2param = NULL;
map = 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(params);
memory->destroy(elem2param); memory->destroy(elem2param);
memory->destroy(forceTable);
memory->destroy(potentialTable);
memory->destroy(neigh3BodyCount);
memory->destroy(neigh3Body);
if (allocated) { if (allocated) {
memory->destroy(setflag); memory->destroy(setflag);
memory->destroy(cutsq); 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) void PairVashishta::compute(int eflag, int vflag)
{ {
validateNeigh3Body();
int i,j,k,ii,jj,kk,inum,jnum,jnumm1; int i,j,k,ii,jj,kk,inum,jnum,jnumm1;
int itype,jtype,ktype,ijparam,ikparam,ijkparam; int itype,jtype,ktype,ijparam,ikparam,ijkparam;
tagint itag,jtag; tagint itag,jtag;
@ -201,8 +111,6 @@ void PairVashishta::compute(int eflag, int vflag)
ytmp = x[i][1]; ytmp = x[i][1];
ztmp = x[i][2]; ztmp = x[i][2];
neigh3BodyCount[i] = 0; // Reset the 3-body neighbor list
// two-body interactions, skip half of them // two-body interactions, skip half of them
jlist = firstneigh[i]; jlist = firstneigh[i];
@ -213,21 +121,6 @@ void PairVashishta::compute(int eflag, int vflag)
j &= NEIGHMASK; j &= NEIGHMASK;
jtag = tag[j]; 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) {
if ((itag+jtag) % 2 == 0) continue; if ((itag+jtag) % 2 == 0) continue;
} else if (itag < jtag) { } 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; 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][0] += delx*fpair;
f[i][1] += dely*fpair; f[i][1] += dely*fpair;
@ -251,8 +154,6 @@ void PairVashishta::compute(int eflag, int vflag)
evdwl,0.0,fpair,delx,dely,delz); evdwl,0.0,fpair,delx,dely,delz);
} }
jlist = neigh3Body[i];
jnum = neigh3BodyCount[i];
jnumm1 = jnum - 1; jnumm1 = jnum - 1;
for (jj = 0; jj < jnumm1; jj++) { 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].cut > cutmax) cutmax = params[m].cut;
if (params[m].r0 > cutmax) cutmax = params[m].r0; if (params[m].r0 > cutmax) cutmax = params[m].r0;
} }
updateTables();
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
void PairVashishta::twobody(const Param &param, double rsq, double &fforce, void PairVashishta::twobody(Param *param, double rsq, double &fforce,
int eflag, double &eng, bool tabulated) int eflag, double &eng)
{ {
if (tabulated) { double r,rinvsq,r4inv,r6inv,reta,lam1r,lam4r,vc2,vc3;
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);
}
const int tableIndex = (rsq - tabinnersq)*oneOverDeltaR2; r = sqrt(rsq);
// double - int will only keep the 0.xxxx part rinvsq = 1.0/rsq;
const double fraction = (rsq - tabinnersq)*oneOverDeltaR2 - tableIndex; 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]; fforce = (param->dvrc*r
double force1 = forceTable[param.ielement][param.jelement][tableIndex+1]; - (4.0*vc3 + lam4r*vc3+param->big6w*r6inv
fforce = (1.0 - fraction)*force0 + fraction*force1; // force is linearly interpolated between the two values - param->heta*reta - vc2 - lam1r*vc2)
if (evflag) { ) * rinvsq;
double energy0 = potentialTable[param.ielement][param.jelement][tableIndex]; if (eflag) eng = param->bigh*reta
double energy1 = potentialTable[param.ielement][param.jelement][tableIndex+1]; + vc2 - vc3 - param->bigw*r6inv
eng = (1.0 - fraction)*energy0 + fraction*energy1; - r*param->dvrc + param->c0;
}
} 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;
}
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
@ -742,15 +620,3 @@ void PairVashishta::threebody(Param *paramij, Param *paramik, Param *paramijk,
if (eflag) eng = facrad; 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 #else
#ifndef LMP_PAIR_Vashishta_H #ifndef LMP_PAIR_VASHISHITA_H
#define LMP_PAIR_Vashishta_H #define LMP_PAIR_VASHISHITA_H
#include "pair.h" #include "pair.h"
@ -28,13 +28,11 @@ class PairVashishta : public Pair {
public: public:
PairVashishta(class LAMMPS *); PairVashishta(class LAMMPS *);
virtual ~PairVashishta(); virtual ~PairVashishta();
virtual void modify_params(int, char **);
virtual void compute(int, int); virtual void compute(int, int);
void settings(int, char **); virtual void settings(int, char **);
void coeff(int, char **); void coeff(int, char **);
virtual double init_one(int, int); double init_one(int, int);
virtual void init_style(); void init_style();
virtual double memory_usage();
protected: protected:
struct Param { struct Param {
@ -48,33 +46,19 @@ class PairVashishta : public Pair {
int ielement,jelement,kelement; 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 double cutmax; // max cutoff for all elements
int nelements; // # of unique elements int nelements; // # of unique elements
char **elements; // names of unique elements char **elements; // names of unique elements
int ***elem2param; // mapping from element triplets to parameters int ***elem2param; // mapping from element triplets to parameters
int *map; // mapping from atom types to elements 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 nparams; // # of stored parameter sets
int maxparam; // max # of parameter sets int maxparam; // max # of parameter sets
Param *params; // parameter set for an I-J-K interaction Param *params; // parameter set for an I-J-K interaction
virtual void allocate(); void allocate();
void read_file(char *); void read_file(char *);
void setup_params(); virtual void setup_params();
void updateTables(); void twobody(Param *, double, double &, int, double &);
void validateNeigh3Body();
void twobody(const Param &, double, double &, int, double &, bool tabulated=false);
void threebody(Param *, Param *, Param *, double, double, double *, double *, void threebody(Param *, Param *, Param *, double, double, double *, double *,
double *, double *, int, double &); double *, double *, int, double &);
}; };

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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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
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;
}

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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.
------------------------------------------------------------------------- */
#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.
*/