From 7d9670bc6c4865d96431e256a0287fc797c971ae Mon Sep 17 00:00:00 2001
From: DallasTrinkle <dtrinkle@illinois.edu>
Date: Fri, 28 Apr 2017 14:48:34 -0500
Subject: [PATCH] Addition of potential, code modifications to incorporate
multicomponent spline MEAM in pair_meam_spline.
Backwards compatible with previous version of pair_meam_spline.
---
potentials/TiO.meam.spline | 130 +++++++
src/USER-MISC/pair_meam_spline.cpp | 601 +++++++++++++++++++----------
src/USER-MISC/pair_meam_spline.h | 50 ++-
3 files changed, 568 insertions(+), 213 deletions(-)
create mode 100644 potentials/TiO.meam.spline
diff --git a/potentials/TiO.meam.spline b/potentials/TiO.meam.spline
new file mode 100644
index 0000000000..ed2a67a962
--- /dev/null
+++ b/potentials/TiO.meam.spline
@@ -0,0 +1,130 @@
+# Ti-O cubic spline potential where O is in the dilute limit. DATE: 2016-06-05 CONTRIBUTOR: Pinchao Zhang, Dallas R. Trinkle
+meam/spline 2 Ti O
+spline3eq
+13
+-20 0
+1.742692837 3.744277175966 99.4865081627958
+2.05580176725 0.910839730906 10.8702523265355
+2.3689106975 0.388045896634 -1.55322418749562
+2.68201962775 -0.018840906533 2.43630041329215
+2.995128558 -0.248098929639 2.67912713976835
+3.30823748825 -0.264489550297 -0.125056384603077
+3.6213464185 -0.227196189283 1.10662555360438
+3.93445534875 -0.129293090176 -0.592053676745914
+4.247564279 -0.059685366933 -0.470123414607672
+4.56067320925 -0.031100025561 -0.0380739973059663
+4.8737821395 -0.013847363202 -0.0711547960695406
+5.18689106975 -0.003203412728 -0.081768292420175
+5.5 0 -0.0571422964883619
+spline3eq
+5
+0.155001355787331 0
+1.9 0.533321679606674 0
+2.8 0.456402081843862 -1.60311717015859
+3.7 -0.324281383502201 1.19940299483249
+4.6 -0.474029826906675 1.47909794595154
+5.5 0 -2.49521499855605
+spline3eq
+13
+0 0
+1.742692837 0 0
+2.05580176725 0 0
+2.3689106975 0 0
+2.68201962775 0 0
+2.995128558 0 0
+3.30823748825 0 0
+3.6213464185 0 0
+3.93445534875 0 0
+4.247564279 0 0
+4.56067320925 0 0
+4.8737821395 0 0
+5.18689106975 0 0
+5.5 0 0
+spline3eq
+11
+-1 0
+2.055801767 1.7475279661 -525.869786904802
+2.2912215903 -5.8677963945 252.796316927755
+2.5266414136 -8.3376288737 71.7318388721015
+2.7620612369 -5.8398712842 -1.93587742753693
+2.9974810602 -3.1140648231 -39.2999192667503
+3.2329008835 -1.7257245065 14.3424136002004
+3.4683207068 -0.4428977017 -29.4925534559498
+3.7037405301 -0.1466643003 -3.18010534572236
+3.9391603534 -0.2095507945 3.33490838803603
+4.1745801767 -0.1442384563 3.71918691359508
+4.41 0 -9.66717019857564
+spline3eq
+5
+-61.9827585211652 0
+1.9 11.2293641315584 0
+2.8 -27.9976343076148 122.648031332411
+3.7 -8.32979773113248 -54.3340881766381
+4.6 -1.00863195297399 3.23150064581724
+5.5 0 -5.3514242228123
+spline3eq
+4
+0.00776934946045395 0.105197706160344
+-55.14233165 -0.29745568008 0.00152870603877451
+-44.7409899033333 -0.15449458722 0.00038933722543571
+-34.3396481566667 0.05098657168 0.00038124926922248
+-23.93830641 0.57342694704 0.0156639264890892
+spline3eq
+5
+-0.00676745157022662 -0.0159520381982146
+-23.9928 0.297607384684645 0
+-15.9241175 0.216691597077105 -0.0024248755353942
+-7.855435 0.0637598673719069 0.00306245895013358
+0.213247499999998 -0.00183450621970427 -0.00177588407633909
+8.28193 -0.111277018874367 0
+spline3eq
+10
+2.77327511656661 0
+2.055801767 -0.1485215264 72.2010867146919
+2.31737934844444 1.6845304918 -47.2744689053404
+2.57895692988889 2.0113365977 -15.1859578405326
+2.84053451133333 1.1444092747 3.33978204841873
+3.10211209277778 0.2861606803 2.587867603808
+3.36368967422222 -0.3459281126 6.14070694084556
+3.62526725566667 -0.6257480601 3.7397696717154
+3.88684483711111 -0.6119510826 4.64749084871402
+4.14842241855556 -0.3112059651 2.83275746415936
+4.41 0 -15.0612086827734
+spline3eq
+5
+12.3315547862781 0
+1.9 2.62105440156724 0
+2.8 10.2850803058354 -25.439802988016
+3.7 3.23933763743897 -7.20203673434025
+4.6 -5.79049355858613 39.5509978688682
+5.5 0 -41.221771373642
+spline3eq
+8
+8.33642274810572 -60.4024574736564
+-1 0.07651409193 -110.652321293778
+-0.724509054371429 0.14155824541 44.8853405500508
+-0.449018108742857 0.75788697341 -25.3065115342002
+-0.173527163114286 0.63011570378 -2.48510144915082
+0.101963782514286 0.09049597305 2.68769386908235
+0.377454728142857 -0.35741586657 -1.01558570129633
+0.652945673771428 -0.65293217647 13.4224786001212
+0.9284366194 -6.00912190653 -452.752542694929
+spline3eq
+5
+0.137191606537625 -1.55094230968985
+-1 0.0513843442016519 0
+-0.5 0.0179024412245673 -2.44986494990154
+0 -0.260650876879273 3.91774583656401
+0.5 -0.190163791764901 -4.84414871911743
+1 -0.763795416646599 0
+spline3eq
+8
+0 0
+-1 0 0
+-0.724509054371429 0 0
+-0.449018108742857 0 0
+-0.173527163114286 0 0
+0.101963782514286 0 0
+0.377454728142857 0 0
+0.652945673771428 0 0
+0.9284366194 0 0
diff --git a/src/USER-MISC/pair_meam_spline.cpp b/src/USER-MISC/pair_meam_spline.cpp
index 614661ad55..4ee5989473 100644
--- a/src/USER-MISC/pair_meam_spline.cpp
+++ b/src/USER-MISC/pair_meam_spline.cpp
@@ -13,6 +13,8 @@
/* ----------------------------------------------------------------------
Contributing author: Alexander Stukowski (LLNL), alex@stukowski.com
+ Will Tipton (Cornell), wwt26@cornell.edu
+ Dallas R. Trinkle (UIUC), dtrinkle@illinois.edu / Pinchao Zhang (UIUC)
see LLNL copyright notice at bottom of file
------------------------------------------------------------------------- */
@@ -23,12 +25,14 @@
* 25-Mar-11 - AS: Fixed calculation of per-atom virial stress.
* 11-Apr-11 - AS: Adapted code to new memory management of LAMMPS.
* 24-Sep-11 - AS: Adapted code to new interface of Error::one() function.
+ * 20-Jun-13 - WT: Added support for multiple species types
+ * 25-Apr-17 - DRT/PZ: Modified format of multiple species type to conform with pairing
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include "math.h"
+#include "stdio.h"
+#include "stdlib.h"
+#include "string.h"
#include "pair_meam_spline.h"
#include "atom.h"
#include "force.h"
@@ -39,6 +43,9 @@
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
+#include <iostream>
+
+using namespace std;
using namespace LAMMPS_NS;
@@ -49,7 +56,6 @@ PairMEAMSpline::PairMEAMSpline(LAMMPS *lmp) : Pair(lmp)
single_enable = 0;
restartinfo = 0;
one_coeff = 1;
- manybody_flag = 1;
nelements = 0;
elements = NULL;
@@ -77,6 +83,15 @@ PairMEAMSpline::~PairMEAMSpline()
if(allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
+
+ delete[] phis;
+ delete[] Us;
+ delete[] rhos;
+ delete[] fs;
+ delete[] gs;
+
+ delete[] zero_atom_energies;
+
delete [] map;
}
}
@@ -85,11 +100,12 @@ PairMEAMSpline::~PairMEAMSpline()
void PairMEAMSpline::compute(int eflag, int vflag)
{
- if (eflag || vflag) ev_setup(eflag, vflag);
- else evflag = vflag_fdotr =
- eflag_global = vflag_global = eflag_atom = vflag_atom = 0;
-
- double cutforcesq = cutoff*cutoff;
+ if (eflag || vflag) {
+ ev_setup(eflag, vflag);
+ } else {
+ evflag = vflag_fdotr = eflag_global = 0;
+ vflag_global = eflag_atom = vflag_atom = 0;
+ }
// Grow per-atom array if necessary
@@ -99,22 +115,13 @@ void PairMEAMSpline::compute(int eflag, int vflag)
memory->create(Uprime_values,nmax,"pair:Uprime");
}
- double** const x = atom->x;
- double** forces = atom->f;
- int nlocal = atom->nlocal;
- bool newton_pair = force->newton_pair;
-
- int inum_full = listfull->inum;
- int* ilist_full = listfull->ilist;
- int* numneigh_full = listfull->numneigh;
- int** firstneigh_full = listfull->firstneigh;
-
// Determine the maximum number of neighbors a single atom has
int newMaxNeighbors = 0;
- for(int ii = 0; ii < inum_full; ii++) {
- int jnum = numneigh_full[ilist_full[ii]];
- if(jnum > newMaxNeighbors) newMaxNeighbors = jnum;
+ for(int ii = 0; ii < listfull->inum; ii++) {
+ int jnum = listfull->numneigh[listfull->ilist[ii]];
+ if(jnum > newMaxNeighbors)
+ newMaxNeighbors = jnum;
}
// Allocate array for temporary bond info
@@ -126,35 +133,129 @@ void PairMEAMSpline::compute(int eflag, int vflag)
}
// Sum three-body contributions to charge density and
- // compute embedding energies
-
- for(int ii = 0; ii < inum_full; ii++) {
- int i = ilist_full[ii];
- double xtmp = x[i][0];
- double ytmp = x[i][1];
- double ztmp = x[i][2];
- int* jlist = firstneigh_full[i];
- int jnum = numneigh_full[i];
- double rho_value = 0;
+ // the embedding energy
+
+ for(int ii = 0; ii < listfull->inum; ii++) {
+ int i = listfull->ilist[ii];
int numBonds = 0;
+
+ // compute charge density and numBonds
+
+ double rho_value = compute_three_body_contrib_to_charge_density(i, numBonds);
+ //cout<<"i "<<i<<" rho "<<rho_value<<" numBonds "<<numBonds<<endl;
+
+ // Compute embedding energy and its derivative
+
+ double Uprime_i = compute_embedding_energy_and_deriv(eflag, i, rho_value);
+ //cout<<"i "<<i<<" U prime "<<Uprime_i<<endl;
+ // Compute three-body contributions to force
+
+ compute_three_body_contrib_to_forces(i, numBonds, Uprime_i);
+
+ }
+
+ // Communicate U'(rho) values
+
+ comm->forward_comm_pair(this);
+
+ // Compute two-body pair interactions
+ compute_two_body_pair_interactions();
+
+ if(vflag_fdotr)
+ virial_fdotr_compute();
+}
+
+
+double PairMEAMSpline::pair_density(int i)
+{
+ double rho_value = 0;
+ MEAM2Body* nextTwoBodyInfo = twoBodyInfo;
+
+ for(int jj = 0; jj < listfull->numneigh[i]; jj++) {
+ int j = listfull->firstneigh[i][jj];
+ j &= NEIGHMASK;
+
+ double jdelx = atom->x[j][0] - atom->x[i][0];
+ double jdely = atom->x[j][1] - atom->x[i][1];
+ double jdelz = atom->x[j][2] - atom->x[i][2];
+ double rij_sq = jdelx*jdelx + jdely*jdely + jdelz*jdelz;
+ double rij = sqrt(rij_sq);
+
+ if(rij_sq < cutoff*cutoff) {
+ double rij = sqrt(rij_sq);
+ rho_value += rhos[i_to_potl(j)].eval(rij);
+ }
+ }
+
+ return rho_value;
+}
+
+
+
+double PairMEAMSpline::three_body_density(int i)
+{
+ double rho_value = 0;
+ int numBonds=0;
+
+ MEAM2Body* nextTwoBodyInfo = twoBodyInfo;
+
+ for(int jj = 0; jj < listfull->numneigh[i]; jj++) {
+ int j = listfull->firstneigh[i][jj];
+ j &= NEIGHMASK;
+
+ double jdelx = atom->x[j][0] - atom->x[i][0];
+ double jdely = atom->x[j][1] - atom->x[i][1];
+ double jdelz = atom->x[j][2] - atom->x[i][2];
+ double rij_sq = jdelx*jdelx + jdely*jdely + jdelz*jdelz;
+
+ if(rij_sq < cutoff*cutoff) {
+ double rij = sqrt(rij_sq);
+ double partial_sum = 0;
+
+ nextTwoBodyInfo->tag = j;
+ nextTwoBodyInfo->r = rij;
+ nextTwoBodyInfo->f = fs[i_to_potl(j)].eval(rij, nextTwoBodyInfo->fprime);
+ nextTwoBodyInfo->del[0] = jdelx / rij;
+ nextTwoBodyInfo->del[1] = jdely / rij;
+ nextTwoBodyInfo->del[2] = jdelz / rij;
+
+ for(int kk = 0; kk < numBonds; kk++) {
+ const MEAM2Body& bondk = twoBodyInfo[kk];
+ double cos_theta = (nextTwoBodyInfo->del[0]*bondk.del[0] +
+ nextTwoBodyInfo->del[1]*bondk.del[1] +
+ nextTwoBodyInfo->del[2]*bondk.del[2]);
+ partial_sum += bondk.f * gs[ij_to_potl(j,bondk.tag)].eval(cos_theta);
+ }
+
+ rho_value += nextTwoBodyInfo->f * partial_sum;
+ numBonds++;
+ nextTwoBodyInfo++;
+ }
+ }
+
+ return rho_value;
+}
+
+double PairMEAMSpline::compute_three_body_contrib_to_charge_density(int i, int& numBonds) {
+ double rho_value = 0;
MEAM2Body* nextTwoBodyInfo = twoBodyInfo;
- for(int jj = 0; jj < jnum; jj++) {
- int j = jlist[jj];
+ for(int jj = 0; jj < listfull->numneigh[i]; jj++) {
+ int j = listfull->firstneigh[i][jj];
j &= NEIGHMASK;
- double jdelx = x[j][0] - xtmp;
- double jdely = x[j][1] - ytmp;
- double jdelz = x[j][2] - ztmp;
+ double jdelx = atom->x[j][0] - atom->x[i][0];
+ double jdely = atom->x[j][1] - atom->x[i][1];
+ double jdelz = atom->x[j][2] - atom->x[i][2];
double rij_sq = jdelx*jdelx + jdely*jdely + jdelz*jdelz;
- if(rij_sq < cutforcesq) {
+ if(rij_sq < cutoff*cutoff) {
double rij = sqrt(rij_sq);
double partial_sum = 0;
nextTwoBodyInfo->tag = j;
nextTwoBodyInfo->r = rij;
- nextTwoBodyInfo->f = f.eval(rij, nextTwoBodyInfo->fprime);
+ nextTwoBodyInfo->f = fs[i_to_potl(j)].eval(rij, nextTwoBodyInfo->fprime);
nextTwoBodyInfo->del[0] = jdelx / rij;
nextTwoBodyInfo->del[1] = jdely / rij;
nextTwoBodyInfo->del[2] = jdelz / rij;
@@ -164,31 +265,41 @@ void PairMEAMSpline::compute(int eflag, int vflag)
double cos_theta = (nextTwoBodyInfo->del[0]*bondk.del[0] +
nextTwoBodyInfo->del[1]*bondk.del[1] +
nextTwoBodyInfo->del[2]*bondk.del[2]);
- partial_sum += bondk.f * g.eval(cos_theta);
+ partial_sum += bondk.f * gs[ij_to_potl(j,bondk.tag)].eval(cos_theta);
}
rho_value += nextTwoBodyInfo->f * partial_sum;
- rho_value += rho.eval(rij);
+ rho_value += rhos[i_to_potl(j)].eval(rij);
numBonds++;
nextTwoBodyInfo++;
}
}
- // Compute embedding energy and its derivative
+ return rho_value;
+}
+double PairMEAMSpline::compute_embedding_energy_and_deriv(int eflag, int i, double rho_value) {
double Uprime_i;
- double embeddingEnergy = U.eval(rho_value, Uprime_i) - zero_atom_energy;
+ double embeddingEnergy = Us[i_to_potl(i)].eval(rho_value, Uprime_i)
+ - zero_atom_energies[i_to_potl(i)];
+ //cout<<"Density "<<rho_value<<endl;
+ //cout<<"embedding energy "<<embeddingEnergy<<endl;
+
+
Uprime_values[i] = Uprime_i;
if(eflag) {
- if(eflag_global) eng_vdwl += embeddingEnergy;
- if(eflag_atom) eatom[i] += embeddingEnergy;
+ if(eflag_global)
+ eng_vdwl += embeddingEnergy;
+ if(eflag_atom)
+ eatom[i] += embeddingEnergy;
}
+ return Uprime_i;
+}
+void PairMEAMSpline::compute_three_body_contrib_to_forces(int i, int numBonds, double Uprime_i) {
double forces_i[3] = {0, 0, 0};
- // Compute three-body contributions to force
-
for(int jj = 0; jj < numBonds; jj++) {
const MEAM2Body bondj = twoBodyInfo[jj];
double rij = bondj.r;
@@ -207,7 +318,7 @@ void PairMEAMSpline::compute(int eflag, int vflag)
bondj.del[1]*bondk->del[1] +
bondj.del[2]*bondk->del[2]);
double g_prime;
- double g_value = g.eval(cos_theta, g_prime);
+ double g_value = gs[ij_to_potl(j,bondk->tag)].eval(cos_theta, g_prime);
double f_rik_prime = bondk->fprime;
double f_rik = bondk->f;
@@ -237,9 +348,9 @@ void PairMEAMSpline::compute(int eflag, int vflag)
forces_i[2] -= fk[2];
int k = bondk->tag;
- forces[k][0] += fk[0];
- forces[k][1] += fk[1];
- forces[k][2] += fk[2];
+ atom->f[k][0] += fk[0];
+ atom->f[k][1] += fk[1];
+ atom->f[k][2] += fk[2];
if(evflag) {
double delta_ij[3];
@@ -254,76 +365,91 @@ void PairMEAMSpline::compute(int eflag, int vflag)
}
}
- forces[i][0] -= forces_j[0];
- forces[i][1] -= forces_j[1];
- forces[i][2] -= forces_j[2];
- forces[j][0] += forces_j[0];
- forces[j][1] += forces_j[1];
- forces[j][2] += forces_j[2];
+ atom->f[i][0] -= forces_j[0];
+ atom->f[i][1] -= forces_j[1];
+ atom->f[i][2] -= forces_j[2];
+ atom->f[j][0] += forces_j[0];
+ atom->f[j][1] += forces_j[1];
+ atom->f[j][2] += forces_j[2];
}
- forces[i][0] += forces_i[0];
- forces[i][1] += forces_i[1];
- forces[i][2] += forces_i[2];
- }
-
- // Communicate U'(rho) values
-
- comm->forward_comm_pair(this);
-
- int inum_half = listhalf->inum;
- int* ilist_half = listhalf->ilist;
- int* numneigh_half = listhalf->numneigh;
- int** firstneigh_half = listhalf->firstneigh;
-
- // Compute two-body pair interactions
+ atom->f[i][0] += forces_i[0];
+ atom->f[i][1] += forces_i[1];
+ atom->f[i][2] += forces_i[2];
+}
- for(int ii = 0; ii < inum_half; ii++) {
- int i = ilist_half[ii];
- double xtmp = x[i][0];
- double ytmp = x[i][1];
- double ztmp = x[i][2];
- int* jlist = firstneigh_half[i];
- int jnum = numneigh_half[i];
+void PairMEAMSpline::compute_two_body_pair_interactions() {
+ for(int ii = 0; ii < listhalf->inum; ii++) {
+ int i = listhalf->ilist[ii];
- for(int jj = 0; jj < jnum; jj++) {
- int j = jlist[jj];
+ for(int jj = 0; jj < listhalf->numneigh[i]; jj++) {
+ int j = listhalf->firstneigh[i][jj];
j &= NEIGHMASK;
double jdel[3];
- jdel[0] = x[j][0] - xtmp;
- jdel[1] = x[j][1] - ytmp;
- jdel[2] = x[j][2] - ztmp;
+ jdel[0] = atom->x[j][0] - atom->x[i][0];
+ jdel[1] = atom->x[j][1] - atom->x[i][1];
+ jdel[2] = atom->x[j][2] - atom->x[i][2];
double rij_sq = jdel[0]*jdel[0] + jdel[1]*jdel[1] + jdel[2]*jdel[2];
- if(rij_sq < cutforcesq) {
+ if(rij_sq < cutoff*cutoff) {
double rij = sqrt(rij_sq);
- double rho_prime;
- rho.eval(rij, rho_prime);
- double fpair = rho_prime * (Uprime_values[i] + Uprime_values[j]);
-
+// double rho_prime;
+// rhos[i_to_potl(j)].eval(rij, rho_prime);
+// cout<<"rho_prime "<<rho_prime<<endl;
+// double fpair = rho_prime * (Uprime_values[i] + Uprime_values[j]);
+ double rho_prime_i,rho_prime_j;
+ rhos[i_to_potl(i)].eval(rij,rho_prime_i);
+ rhos[i_to_potl(j)].eval(rij,rho_prime_j);
+ double fpair = rho_prime_j * Uprime_values[i] + rho_prime_i*Uprime_values[j];
+ //cout<<"fpair "<<fpair<<endl;
double pair_pot_deriv;
- double pair_pot = phi.eval(rij, pair_pot_deriv);
- fpair += pair_pot_deriv;
+ double pair_pot = phis[ij_to_potl(i,j)].eval(rij, pair_pot_deriv);
+ //cout<<"pair potential "<<pair_pot<<endl;
+ //cout<<"pair pot_deriv "<<pair_pot_deriv<<endl;
+
+ fpair += pair_pot_deriv;
// Divide by r_ij to get forces from gradient
fpair /= rij;
- forces[i][0] += jdel[0]*fpair;
- forces[i][1] += jdel[1]*fpair;
- forces[i][2] += jdel[2]*fpair;
- forces[j][0] -= jdel[0]*fpair;
- forces[j][1] -= jdel[1]*fpair;
- forces[j][2] -= jdel[2]*fpair;
- if (evflag) ev_tally(i, j, nlocal, newton_pair,
+ atom->f[i][0] += jdel[0]*fpair;
+ //cout<<i<<"pair fx "<<atom->f[i][0]<<endl;
+ atom->f[i][1] += jdel[1]*fpair;
+ //cout<<i<<"pair fy "<<atom->f[i][1]<<endl;
+ atom->f[i][2] += jdel[2]*fpair;
+ //cout<<i<<"pair fz "<<atom->f[i][2]<<endl;
+ atom->f[j][0] -= jdel[0]*fpair;
+ //cout<<j<<"pair fx "<<atom->f[j][0]<<endl;
+ atom->f[j][1] -= jdel[1]*fpair;
+ //cout<<j<<"pair fy "<<atom->f[j][1]<<endl;
+ atom->f[j][2] -= jdel[2]*fpair;
+ ////cout<<j<<"pair fz "<<atom->f[j][2]<<endl;
+ if (evflag) ev_tally(i, j, atom->nlocal, force->newton_pair,
pair_pot, 0.0, -fpair, jdel[0], jdel[1], jdel[2]);
}
}
}
+}
- if(vflag_fdotr) virial_fdotr_compute();
+/* ----------------------------------------------------------------------
+ helper functions to map atom types to potential array indices
+------------------------------------------------------------------------- */
+
+int PairMEAMSpline::ij_to_potl(int i, int j) {
+ int n = atom->ntypes;
+ int itype = atom->type[i];
+ int jtype = atom->type[j];
+
+ // printf("%d %d %d\n",n,itype,jtype);
+ return jtype - 1 + (itype-1)*n - (itype-1)*itype/2;
+}
+
+int PairMEAMSpline::i_to_potl(int i) {
+ int itype = atom->type[i];
+ return itype - 1;
}
/* ---------------------------------------------------------------------- */
@@ -331,11 +457,23 @@ void PairMEAMSpline::compute(int eflag, int vflag)
void PairMEAMSpline::allocate()
{
allocated = 1;
- int n = atom->ntypes;
+ int n = nelements;
memory->create(setflag,n+1,n+1,"pair:setflag");
memory->create(cutsq,n+1,n+1,"pair:cutsq");
+ int nmultichoose2 = n*(n+1)/2;
+ //Change the functional form
+ //f_ij->f_i
+ //g_i(cos\theta_ijk)->g_jk(cos\theta_ijk)
+ phis = new SplineFunction[nmultichoose2];
+ Us = new SplineFunction[n];
+ rhos = new SplineFunction[n];
+ fs = new SplineFunction[n];
+ gs = new SplineFunction[nmultichoose2];
+
+ zero_atom_energies = new double[n];
+
map = new int[n+1];
}
@@ -356,7 +494,8 @@ void PairMEAMSpline::coeff(int narg, char **arg)
{
int i,j,n;
- if (!allocated) allocate();
+ if (!allocated)
+ allocate();
if (narg != 3 + atom->ntypes)
error->all(FLERR,"Incorrect args for pair coefficients");
@@ -366,45 +505,34 @@ void PairMEAMSpline::coeff(int narg, char **arg)
if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
error->all(FLERR,"Incorrect args for pair coefficients");
+ // read potential file: also sets the number of elements.
+ read_file(arg[2]);
+
// read args that map atom types to elements in potential file
// map[i] = which element the Ith atom type is, -1 if NULL
// nelements = # of unique elements
// elements = list of element names
- if (elements) {
- for (i = 0; i < nelements; i++) delete [] elements[i];
- delete [] elements;
- }
- elements = new char*[atom->ntypes];
- for (i = 0; i < atom->ntypes; i++) elements[i] = NULL;
-
- nelements = 0;
- for (i = 3; i < narg; i++) {
- if (strcmp(arg[i],"NULL") == 0) {
- map[i-2] = -1;
- continue;
- }
- for (j = 0; j < nelements; j++)
- if (strcmp(arg[i],elements[j]) == 0) break;
- map[i-2] = j;
- if (j == nelements) {
- n = strlen(arg[i]) + 1;
- elements[j] = new char[n];
- strcpy(elements[j],arg[i]);
- nelements++;
+ if ((nelements == 1) && (strlen(elements[0]) == 0)) {
+ // old style: we only have one species, so we're either "NULL" or we match.
+ for (i = 3; i < narg; i++)
+ if (strcmp(arg[i],"NULL") == 0)
+ map[i-2] = -1;
+ else
+ map[i-2] = 0;
+ } else {
+ for (i = 3; i < narg; i++) {
+ if (strcmp(arg[i],"NULL") == 0) {
+ map[i-2] = -1;
+ continue;
+ }
+ for (j = 0; j < nelements; j++)
+ if (strcmp(arg[i],elements[j]) == 0)
+ break;
+ if (j < nelements) map[i-2] = j;
+ else error->all(FLERR,"No matching element in EAM potential file");
+ }
}
- }
-
- // for now, only allow single element
-
- if (nelements > 1)
- error->all(FLERR,
- "Pair meam/spline only supports single element potentials");
-
- // read potential file
-
- read_file(arg[2]);
-
// clear setflag since coeff() called once with I,J = * *
n = atom->ntypes;
@@ -425,65 +553,134 @@ void PairMEAMSpline::coeff(int narg, char **arg)
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
-/* ----------------------------------------------------------------------
- set coeffs for one or more type pairs
-------------------------------------------------------------------------- */
-
#define MAXLINE 1024
void PairMEAMSpline::read_file(const char* filename)
{
- if(comm->me == 0) {
- FILE *fp = force->open_potential(filename);
- if(fp == NULL) {
- char str[1024];
- sprintf(str,"Cannot open spline MEAM potential file %s", filename);
- error->one(FLERR,str);
- }
-
- // Skip first line of file.
- char line[MAXLINE];
- fgets(line, MAXLINE, fp);
-
- // Parse spline functions.
- phi.parse(fp, error);
- rho.parse(fp, error);
- U.parse(fp, error);
- f.parse(fp, error);
- g.parse(fp, error);
-
- fclose(fp);
- }
-
- // Transfer spline functions from master processor to all other processors.
- phi.communicate(world, comm->me);
- rho.communicate(world, comm->me);
- f.communicate(world, comm->me);
- U.communicate(world, comm->me);
- g.communicate(world, comm->me);
-
- // Calculate 'zero-point energy' of single atom in vacuum.
- zero_atom_energy = U.eval(0.0);
-
- // Determine maximum cutoff radius of all relevant spline functions.
- cutoff = 0.0;
- if(phi.cutoff() > cutoff) cutoff = phi.cutoff();
- if(rho.cutoff() > cutoff) cutoff = rho.cutoff();
- if(f.cutoff() > cutoff) cutoff = f.cutoff();
-
- // Set LAMMPS pair interaction flags.
- for(int i = 1; i <= atom->ntypes; i++) {
- for(int j = 1; j <= atom->ntypes; j++) {
- setflag[i][j] = 1;
- cutsq[i][j] = cutoff;
- }
- }
+ int nmultichoose2; // = (n+1)*n/2;
+
+ if(comm->me == 0) {
+ FILE *fp = fopen(filename, "r");
+ if(fp == NULL) {
+ char str[1024];
+ sprintf(str,"Cannot open spline MEAM potential file %s", filename);
+ error->one(FLERR,str);
+ }
+
+ // Skip first line of file. It's a comment.
+ char line[MAXLINE];
+ fgets(line, MAXLINE, fp);
+
+ // Second line holds potential type (currently just "meam/spline") in new potential format.
+ bool isNewFormat;
+ long loc = ftell(fp);
+ fgets(line, MAXLINE, fp);
+ if (strncmp(line, "meam/spline", 11) == 0) {
+ isNewFormat = true;
+ // parse the rest of the line!
+ char *linep = line+12, *word;
+ const char *sep = " ,;:-\t\n"; // overkill, but safe
+ word = strsep(&linep, sep);
+ if (! *word)
+ error->one(FLERR, "Need to include number of atomic species on meam/spline line in potential file");
+ int n = atoi(word);
+ if (n<1)
+ error->one(FLERR, "Invalid number of atomic species on meam/spline line in potential file");
+ nelements = n;
+ elements = new char*[n];
+ for (int i=0; i<n; ++i) {
+ word = strsep(&linep, sep);
+ if (! *word)
+ error->one(FLERR, "Not enough atomic species in meam/spline\n");
+ elements[i] = new char[strlen(word)+1];
+ strcpy(elements[i], word);
+ }
+ } else {
+ isNewFormat = false;
+ nelements = 1; // old format only handles one species anyway; this is for backwards compatibility
+ elements = new char*[1];
+ elements[0] = new char[1];
+ strcpy(elements[0], "");
+ fseek(fp, loc, SEEK_SET);
+ }
+
+ nmultichoose2 = ((nelements+1)*nelements)/2;
+ // allocate!!
+ allocate();
+
+ // Parse spline functions.
+
+ for (int i = 0; i < nmultichoose2; i++)
+ phis[i].parse(fp, error, isNewFormat);
+ for (int i = 0; i < nelements; i++)
+ rhos[i].parse(fp, error, isNewFormat);
+ for (int i = 0; i < nelements; i++)
+ Us[i].parse(fp, error, isNewFormat);
+ for (int i = 0; i < nelements; i++)
+ fs[i].parse(fp, error, isNewFormat);
+ for (int i = 0; i < nmultichoose2; i++)
+ gs[i].parse(fp, error, isNewFormat);
+
+ fclose(fp);
+ }
- //phi.writeGnuplot("phi.gp", "Phi(r)");
- //rho.writeGnuplot("rho.gp", "Rho(r)");
- //f.writeGnuplot("f.gp", "f(r)");
- //U.writeGnuplot("U.gp", "U(rho)");
- //g.writeGnuplot("g.gp", "g(x)");
+ // Transfer spline functions from master processor to all other processors.
+ MPI_Bcast(&nelements, 1, MPI_INT, 0, world);
+ MPI_Bcast(&nmultichoose2, 1, MPI_INT, 0, world);
+ // allocate!!
+ if (!allocated) {
+ allocate();
+ elements = new char*[nelements];
+ }
+ for (int i = 0; i < nelements; ++i) {
+ int n;
+ if (comm->me == 0)
+ n = strlen(elements[i]);
+ MPI_Bcast(&n, 1, MPI_INT, 0, world);
+ if (comm->me != 0)
+ elements[i] = new char[n];
+ MPI_Bcast(elements[i], n, MPI_CHAR, 0, world);
+ }
+ for (int i = 0; i < nmultichoose2; i++)
+ phis[i].communicate(world, comm->me);
+ for (int i = 0; i < nelements; i++)
+ rhos[i].communicate(world, comm->me);
+ for (int i = 0; i < nelements; i++)
+ fs[i].communicate(world, comm->me);
+ for (int i = 0; i < nelements; i++)
+ Us[i].communicate(world, comm->me);
+ for (int i = 0; i < nmultichoose2; i++)
+ gs[i].communicate(world, comm->me);
+
+ // Calculate 'zero-point energy' of single atom in vacuum.
+ for (int i = 0; i < nelements; i++)
+ zero_atom_energies[i] = Us[i].eval(0.0);
+
+ // Determine maximum cutoff radius of all relevant spline functions.
+ cutoff = 0.0;
+ for (int i = 0; i < nmultichoose2; i++)
+ if(phis[i].cutoff() > cutoff)
+ cutoff = phis[i].cutoff();
+ for (int i = 0; i < nelements; i++)
+ if(rhos[i].cutoff() > cutoff)
+ cutoff = rhos[i].cutoff();
+ for (int i = 0; i < nelements; i++)
+ if(fs[i].cutoff() > cutoff)
+ cutoff = fs[i].cutoff();
+
+ // Set LAMMPS pair interaction flags.
+ for(int i = 1; i <= atom->ntypes; i++) {
+ for(int j = 1; j <= atom->ntypes; j++) {
+ // setflag[i][j] = 1;
+ cutsq[i][j] = cutoff; // should this be squared?
+ }
+ }
+
+ //phi.writeGnuplot("phi.gp", "Phi(r)");
+ //rho.writeGnuplot("rho.gp", "Rho(r)");
+ //f.writeGnuplot("f.gp", "f(r)");
+ //U.writeGnuplot("U.gp", "U(rho)");
+ //g.writeGnuplot("g.gp", "g(x)");
}
/* ----------------------------------------------------------------------
@@ -495,12 +692,15 @@ void PairMEAMSpline::init_style()
error->all(FLERR,"Pair style meam/spline requires newton pair on");
// Need both full and half neighbor list.
- int irequest_full = neighbor->request(this,instance_me);
+ int irequest_full = neighbor->request(this);
neighbor->requests[irequest_full]->id = 1;
neighbor->requests[irequest_full]->half = 0;
neighbor->requests[irequest_full]->full = 1;
- int irequest_half = neighbor->request(this,instance_me);
+ int irequest_half = neighbor->request(this);
neighbor->requests[irequest_half]->id = 2;
+ // neighbor->requests[irequest_half]->half = 0;
+ // neighbor->requests[irequest_half]->half_from_full = 1;
+ // neighbor->requests[irequest_half]->otherlist = irequest_full;
}
/* ----------------------------------------------------------------------
@@ -523,14 +723,13 @@ double PairMEAMSpline::init_one(int i, int j)
/* ---------------------------------------------------------------------- */
-int PairMEAMSpline::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+int PairMEAMSpline::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
{
int* list_iter = list;
int* list_iter_end = list + n;
while(list_iter != list_iter_end)
*buf++ = Uprime_values[*list_iter++];
- return n;
+ return 1;
}
/* ---------------------------------------------------------------------- */
@@ -563,10 +762,14 @@ double PairMEAMSpline::memory_usage()
/// Parses the spline knots from a text file.
-void PairMEAMSpline::SplineFunction::parse(FILE* fp, Error* error)
+void PairMEAMSpline::SplineFunction::parse(FILE* fp, Error* error, bool isNewFormat)
{
char line[MAXLINE];
+ // If new format, read the spline format. Should always be "spline3eq" for now.
+ if (isNewFormat)
+ fgets(line, MAXLINE, fp);
+
// Parse number of spline knots.
fgets(line, MAXLINE, fp);
int n = atoi(line);
@@ -578,9 +781,11 @@ void PairMEAMSpline::SplineFunction::parse(FILE* fp, Error* error)
double d0 = atof(strtok(line, " \t\n\r\f"));
double dN = atof(strtok(NULL, " \t\n\r\f"));
init(n, d0, dN);
+//printf("%s\n",line);
- // Skip line.
- fgets(line, MAXLINE, fp);
+ // Skip line in old format
+ if (!isNewFormat)
+ fgets(line, MAXLINE, fp);
// Parse knot coordinates.
for(int i=0; i<n; i++) {
@@ -734,3 +939,5 @@ void PairMEAMSpline::SplineFunction::writeGnuplot(const char* filename, const ch
* Lawrence Livermore National Security, LLC, and shall not be used for
* advertising or product endorsement purposes.
------------------------------------------------------------------------- */
+
+
diff --git a/src/USER-MISC/pair_meam_spline.h b/src/USER-MISC/pair_meam_spline.h
index d16a321cb6..3d09cce23b 100644
--- a/src/USER-MISC/pair_meam_spline.h
+++ b/src/USER-MISC/pair_meam_spline.h
@@ -1,4 +1,4 @@
-/* -*- c++ -*- ----------------------------------------------------------
+/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
@@ -43,10 +43,24 @@ public:
virtual void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
+ void get_coeff(double *, double *);
+ double pair_density(int );
+ double three_body_density(int );
void init_style();
void init_list(int, class NeighList *);
double init_one(int, int);
+ // helper functions for compute()
+
+ double compute_three_body_contrib_to_charge_density(int i, int& numBonds); // returns rho_value and returns numBonds by reference
+ double compute_embedding_energy_and_deriv(int eflag, int i, double rho_value); // returns the derivative of the embedding energy Uprime_i
+ void compute_three_body_contrib_to_forces(int i, int numBonds, double Uprime_i);
+ void compute_two_body_pair_interactions();
+
+ int ij_to_potl(int i, int j);
+ int i_to_potl(int i);
+
+
int pack_forward_comm(int, int *, double *, int, int *);
void unpack_forward_comm(int, int, double *);
int pack_reverse_comm(int, int, double *);
@@ -74,15 +88,15 @@ protected:
}
/// Initialization of spline function.
- void init(int _n, double _deriv0, double _derivN) {
- N = _n;
+ void init(int _N, double _deriv0, double _derivN) {
+ N = _N;
deriv0 = _deriv0;
derivN = _derivN;
- delete[] X;
- delete[] Xs;
- delete[] Y;
- delete[] Y2;
- delete[] Ydelta;
+ // if (X) delete[] X;
+ // if (Xs) delete[] Xs;
+ // if (Y) delete[] Y;
+ // if (Y2) delete[] Y2;
+ // if (Ydelta) delete[] Ydelta;
X = new double[N];
Xs = new double[N];
Y = new double[N];
@@ -97,7 +111,7 @@ protected:
int numKnots() const { return N; }
/// Parses the spline knots from a text file.
- void parse(FILE* fp, Error* error);
+ void parse(FILE* fp, Error* error, bool isNewFormat);
/// Calculates the second derivatives of the cubic spline.
void prepareSpline(Error* error);
@@ -209,18 +223,18 @@ protected:
/// Helper data structure for potential routine.
struct MEAM2Body {
- int tag;
+ int tag; // holds the index of the second atom (j)
double r;
double f, fprime;
double del[3];
};
- SplineFunction phi; // Phi(r_ij)
- SplineFunction rho; // Rho(r_ij)
- SplineFunction f; // f(r_ij)
- SplineFunction U; // U(rho)
- SplineFunction g; // g(cos_theta)
- double zero_atom_energy; // Shift embedding energy by this value to make it zero for a single atom in vacuum.
+ SplineFunction* phis; // Phi_i(r_ij)
+ SplineFunction* rhos; // Rho_ij(r_ij)
+ SplineFunction* fs; // f_i(r_ij)
+ SplineFunction* Us; // U_i(rho)
+ SplineFunction* gs; // g_ij(cos_theta)
+ double* zero_atom_energies; // Shift embedding energy by this value to make it zero for a single atom in vacuum.
double cutoff; // The cutoff radius
@@ -231,6 +245,8 @@ protected:
void read_file(const char* filename);
void allocate();
+
+
};
}
@@ -279,3 +295,5 @@ protected:
*
* See file 'pair_spline_meam.cpp' for history of changes.
------------------------------------------------------------------------- */
+
+
--
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