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pair_mgpt.h
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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 authors: Tomas Oppelstrup, LLNL (oppelstrup2@llnl.gov)
and John Moriarty, LLNL (moriarty2@llnl.gov)
Fast MGPT algorithm developed by Tomas Oppelstrup (2015) based on the
matrix MGPT v4.4 FORTRAN routine of John Moriarty (2006) as converted
to C++ for LAMMPS application by Jamie Marian and Alexander Stukowski
(2011). See LLNL copyright notice at bottom of this file.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(mgpt,PairMGPT)
#else
#ifndef LMP_PAIR_MGPT_H
#define LMP_PAIR_MGPT_H
#include <new>
#include <cmath>
#include <cstdio>
#include <cassert>
#include "pair.h"
#include "domain.h"
#include "mgpt_readpot.h"
#include "mgpt_linalg.h"
namespace LAMMPS_NS {
class PairMGPT : public Pair {
mgpt_linalg linalg;
public:
class Doublet {
public:
int i,j;
public:
Doublet(const Doublet &t) : i(t.i),j(t.j) {}
Doublet(int ii,int jj) : i(ii < jj ? ii:jj),j(ii < jj ? jj : ii) {}
Doublet operator=(const Doublet &t) {
i = t.i;
j = t.j;
return *this;
}
int operator==(const Doublet &b) const {
return (i == b.i) && (j == b.j);
}
int hash() const { return i*333331 + j*331; }
};
template<typename T,typename K> class Hash {
class Link {
public:
T data;
Link *next;
K key;
int hits;
Link(const K &k,Link *n) : next(n),key(k),hits(1) {}
static void *operator new(std::size_t sz) {
const size_t align = 32;
size_t x = (size_t) (void *) ::operator new(sz+align);
size_t y = (x + align) - ((x+align)&(align-1));
assert(sizeof(void *) <= align);
assert((x & (sizeof(void *)-1)) == 0);
((void **) y)[-1] = (void *) x;
return (void *) y;
}
static void operator delete(void *ptr) {
::operator delete(((void **) ptr)[-1]);
}
};
int isprime(int x) {
if(x%2 == 0)
return 0;
else {
int k = 3;
while(k*k <= x) {
if(x%k == 0) return 0;
k = k+2;
}
return 1;
}
}
int size,used;
Link **table;
int maxlength,nstep,nsearch;
public:
class Iterator {
Hash &H;
int idx;
Link *p;
public:
Iterator(Hash &HH) : H(HH),idx(-1),p(0) { next(); }
Iterator(Hash &HH,int iidx,Link *pp) : H(HH),idx(iidx),p(pp) {}
void next() {
if(idx >= H.Size()) return;
if(p != 0) p = p->next;
if(p == 0) {
do {
idx = idx+1;
if(idx >= H.Size()) return;
p = H.table[idx];
} while(p == 0);
}
}
K *key() { return &p->key; }
T *data() { return &p->data; }
Link *link() { return p; }
int operator==(const Iterator &a) {
return idx==a.idx && p==a.p;
}
int operator!=(const Iterator &a) {
return !(*this == a);
}
};
Hash(int sz) {
while(!isprime(sz)) sz = sz + 1;
size = sz;
used = 0;
table = new Link *[size];
for(int i = 0; i<size; i++)
table[i] = 0;
/* Counters for statistics */
maxlength = 0;
nstep = 0;
nsearch = 0;
}
~Hash() {
for(int i = 0; i<size; i++) {
Link *p = table[i];
while(p != 0) {
Link *q = p->next;
delete p;
p = q;
}
}
delete[] table;
}
Iterator begin() { return Iterator(*this); }
Iterator end() { return Iterator(*this,size,0); }
int Size() { return size; }
int Used() { return used; }
int NSearch() { return nsearch; }
int MaxLength() { return maxlength; }
int NStep() { return nstep; }
T * Insert(const K &key) {
int idx = key.hash() % size;
if(idx < 0) idx = idx + size;
if(idx >= size || idx < 0) {
printf("(1) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size);
exit(1);
}
used = used + 1;
if(1) {
table[idx] = new Link(key,table[idx]);
return &table[idx]->data;
} else { /* This is for threading... and incomplete */
typedef Link *LinkPtr;
LinkPtr ptr = table[idx],last = 0,dataptr = new Link(key,0);
while(ptr != 0) {
last = ptr;
ptr = ptr->next;
}
*((volatile LinkPtr *) &(last->next)) = dataptr;
return &(dataptr->data);
}
}
void Remove(const K &key) {
int idx = key.hash() % size;
Link *p,*last = 0;
int count = 1;
if(idx < 0) idx = idx + size;
if(idx >= size || idx < 0) {
printf("(2) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size);
exit(1);
}
p = table[idx];
while(p != 0 && !(p->key == key)) {
last = p;
p = p->next;
count = count + 1;
}
if(p != 0) {
used = used - 1;
if(last == 0)
table[idx] = p->next;
else
last->next = p->next;
delete p;
}
if(count > maxlength)
maxlength = count;
nsearch = nsearch + 1;
nstep = nstep + count;
}
T * Lookup(const K &key) {
int idx = key.hash() % size;
Link *p;
int count = 1;
if(idx < 0) idx = idx + size;
if(idx >= size || idx < 0) {
printf("(3) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size);
exit(1);
}
p = table[idx];
while(p != 0 && !(p->key == key)) {
p = p->next;
count = count + 1;
}
if(count > maxlength)
maxlength = count;
nsearch = nsearch + 1;
nstep = nstep + count;
if(p != 0) p->hits++;
return (p == 0) ? 0 : &p->data;
}
};
public:
PairMGPT(class LAMMPS *);
~PairMGPT();
void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
void init_style();
void init_list(int, class NeighList *);
double init_one(int, int);
private:
void read_files(const char* parminFile, const char* potinFile, double vol);
void allocate();
struct Matrix {
static int sz;
double m[8][8];
int align_check() {
return ((((unsigned long long int) m) & 31) > 0);
}
void zero() {
for(int i = 0; i<8; i++)
for(int j = 0; j<8; j++)
m[i][j] = 0.0;
}
void operator=(const Matrix &A) {
for(int i = 1; i<=sz; i++)
for(int j = 1; j<=sz; j++)
m[i][j] = A.m[i][j];
}
void operator=(double x) {
for(int i = 1; i<=sz; i++)
for(int j = 1; j<=sz; j++)
m[i][j] = x;
}
Matrix operator+(const Matrix &B) const {
Matrix s;
for(int i = 1; i<=sz; i++)
for(int j = 1; j<=sz; j++)
s.m[i][j] = m[i][j] + B.m[i][j];
return s;
}
Matrix operator-(const Matrix &B) const {
Matrix s;
for(int i = 1; i<=sz; i++)
for(int j = 1; j<=sz; j++)
s.m[i][j] = m[i][j] - B.m[i][j];
return s;
}
Matrix operator-() const {
Matrix s;
for(int i = 1; i<=sz; i++)
for(int j = 1; j<=sz; j++)
s.m[i][j] = -m[i][j];
return s;
}
Matrix operator*(double x) const {
Matrix P;
for(int i = 1; i<=sz; i++)
for(int j = 0; j<=sz; j++)
P.m[i][j] = m[i][j] * x;
return P;
}
Matrix operator/(double x) const {
return (*this) * (1.0/x);
}
Matrix transpose() const {
Matrix T;
for(int i = 1; i<=sz; i++)
for(int j = 1; j<=sz; j++)
T.m[j][i] = m[i][j];
return T;
}
};
Matrix transpose(const Matrix &A) { return A.transpose(); }
/* Preprocessor stuff to set alignment requirements on bonda_data
and triplet_data structures. Without alignmnt, optimized algebra
routines can fail.
*/
#ifdef __GNUC__
#define PREALIGN struct
#define POSTALIGN __attribute__((__aligned__(32)))
#elif defined(__bgq__)
#define PREALIGN __align(32) struct
#define POSTALIGN
#elif defined(__INTEL_COMPILER)
/* This will probably not be used, since the Intel compiler also defines __GNUC__ */
#define PREALIGN struct __declspec(align(32))
#define POSTALIGN
#else
/* Try GNU syntax anyway... */
#define PREALIGN struct
#define POSTALIGN __attribute__((__aligned__(32)))
/*
#define PREALIGN struct
#define POSTALIGN
*/
#endif
PREALIGN /*struct*/ bond_data {
Matrix H,Hx,Hy,Hz;
double fl_deriv_sum;
double pad[3];
} POSTALIGN;
PREALIGN /*struct*/ triplet_data {
Matrix H1H2;
Matrix H1xH2 , H1yH2 , H1zH2;
Matrix H1H2x , H1H2y , H1H2z;
int align_check() {
return
(H1H2.align_check() << 0) |
(H1xH2.align_check() << 1) |
(H1yH2.align_check() << 2) |
(H1zH2.align_check() << 3) |
(H1H2x.align_check() << 4) |
(H1H2y.align_check() << 5) |
(H1H2z.align_check() << 6) ;
}
void zero() {
H1H2.zero();
H1xH2.zero(); H1yH2.zero(); H1zH2.zero();
H1H2x.zero(); H1H2y.zero(); H1H2z.zero();
}
} POSTALIGN;
#undef PREALIGN
#undef POSTALIGN
void make_bond(const double xx[][3],int i,int j,bond_data *bptr);
void make_triplet(bond_data *ij_bond,bond_data *ik_bond,triplet_data *triptr);
triplet_data *get_triplet(const double xx[][3],int i,int j,int k,
Hash<bond_data,Doublet> *bhash,triplet_data *twork,
double *dvir_ij_p,double *dvir_ik_p);
int c1_outside(const double a[3],
int triclinic,const double alpha[3]) {
const double stol = 1e-5;
if(triclinic) {
for(int p = 0; p<3; p++) {
double cog = a[p];
if(cog < domain->sublo_lamda[p]-0.5*rmax*alpha[p]-stol) return 1;
if(cog > domain->subhi_lamda[p]+0.5*rmax*alpha[p]+stol) return 1;
}
} else {
double rout = 0.0;
for(int p = 0; p<3; p++) {
double cog = a[p];
if(cog < domain->sublo[p]-0.5*rmax-stol) return 1;
if(cog > domain->subhi[p]+0.5*rmax+stol) return 1;
if(cog < domain->sublo[p]-stol) {
double t = cog - (domain->sublo[p]-stol);
rout = rout + t*t;
} else if(cog > domain->subhi[p]+stol) {
double t = cog - (domain->subhi[p]+stol);
rout = rout + t*t;
}
}
if(rout > 0.25*rmax*rmax)
return 1;
}
return 0;
}
int c2_outside(const double a[3],const double b[3],
int triclinic,const double alpha[3]) {
const double stol = 1e-5;
if(triclinic) {
for(int p = 0; p<3; p++) {
double cog = 0.5*(a[p] + b[p]);
if(cog < domain->sublo_lamda[p]-0.5*rcrit*alpha[p]-stol) return 1;
if(cog > domain->subhi_lamda[p]+0.5*rcrit*alpha[p]+stol) return 1;
}
} else {
double rout = 0.0;
for(int p = 0; p<3; p++) {
double cog = 0.5*(a[p] + b[p]);
if(cog < domain->sublo[p]-0.5*rcrit-stol) return 1;
if(cog > domain->subhi[p]+0.5*rcrit+stol) return 1;
if(cog < domain->sublo[p]-stol) {
double t = cog - (domain->sublo[p]-stol);
rout = rout + t*t;
} else if(cog > domain->subhi[p]+stol) {
double t = cog - (domain->subhi[p]+stol);
rout = rout + t*t;
}
}
if(rout > 0.25*rcrit*rcrit)
return 1;
}
return 0;
}
double get_weight(const int triclinic,
const double a[3] = 0,const double b[3] = 0,
const double c[3] = 0,const double d[3] = 0) {
const double
*s0 = triclinic ? domain->sublo_lamda : domain->sublo,
*s1 = triclinic ? domain->subhi_lamda : domain->subhi;
double weight = 1.0;
const double stol = 1e-5;
for(int p = 0; p<3; p++) {
double cog = 0.0,q,w,n = 0.0;
if(a != 0) { cog = cog + a[p]; n = n + 1; }
if(b != 0) { cog = cog + b[p]; n = n + 1; }
if(c != 0) { cog = cog + c[p]; n = n + 1; }
if(d != 0) { cog = cog + d[p]; n = n + 1; }
cog = cog * (1.0/n);
if(cog < 0.5*(s0[p]+s1[p])) q = cog - s0[p];
else q = s1[p] - cog;
w = q*(0.5/stol) + 0.5;
if(w > 1.0) w = 1.0;
if(w < 0.0) w = 0.0;
weight = weight * w;
}
return weight;
}
void force_debug_3t(double xx[][3],
int i0,int j0,int k0,
int i ,int j ,int k ,
double dfix,double dfiy,double dfiz,
double dfjx,double dfjy,double dfjz,
double dfkx,double dfky,double dfkz);
void force_debug_3v(double xx[][3],
int i0,int j0,int k0,
int i ,int j ,int k ,
double dfix,double dfiy,double dfiz,
double dfjx,double dfjy,double dfjz,
double dfkx,double dfky,double dfkz);
void force_debug_4(double xx[][3],
int i0,int j0,int k0,int m0,
int i ,int j ,int k ,int m ,
double dfix,double dfiy,double dfiz,
double dfjx,double dfjy,double dfjz,
double dfkx,double dfky,double dfkz,
double dfmx,double dfmy,double dfmz);
double numderiv3t(double xx[][3],int i,int j,int k,int p);
double numderiv3v(double xx[][3],int i,int j,int k,int p,int ipert);
double numderiv4(double xx[][3],int i,int j,int k,int m,int p);
void compute_x(const int *nnei,const int * const *nlist,
double *e_s,double *e_p,double *e_t,double *e_q,
int evflag,int newton_pair);
/* Reimplementation of bond matrix computation */
void fl_deriv_new(double r,double ri,double xhat,double yhat,double zhat,
double &fl_0,double &fl_x,double &fl_y,double &fl_z,
double &fl_rp,double &fl_p1,double &fl_r0,double &fl_al);
void hamltn_5_raw(const double xin,const double yin,const double zin,
double M [8][8],double Mx[8][8],
double My[8][8],double Mz[8][8],
double *fl_deriv_sum_p);
void hamltn_7_raw(const double xin,const double yin,const double zin,
double M [8][8],double Mx[8][8],
double My[8][8],double Mz[8][8],
double *fl_deriv_sum_p);
/* * */
// Old matrix routines, only used in force debug routines.
/// This function calculates the matrix product of ha and hb.
inline Matrix prodmat(const Matrix& ha, const Matrix& hb) const {
Matrix h;
for(int l = 1; l <= lmax; l++) {
for(int n = 1; n <= lmax; n++) {
h.m[l][n] = 0.0;
for(int m = 1; m <= lmax; m++)
h.m[l][n] += ha.m[l][m] * hb.m[m][n];
}
}
return h;
}
/// This function calculates the trace of the matrix product of ha and hb.
inline double trace(const Matrix& ha, const Matrix& hb) const {
double zquan = 0.0;
for(int n = 1; n <= lmax; n++) {
double cquan = 0.0;
for(int m = 1; m <= lmax; m++)
cquan += ha.m[n][m] * hb.m[m][n];
zquan += cquan;
}
return zquan;
}
/* * */
inline void transprod(const Matrix& a,const Matrix& b,Matrix &c) const
{
int i,j,k;
if(lmax == 5) {
const int n = 5;
for(i = 1; i<=n; i++)
for(j = 1; j<=n; j++) {
double s = 0.0;
for(k = 1; k<=n; k++)
s = s + a.m[i][k]*b.m[j][k];
c.m[i][j] = s;
}
} else if(lmax == 7) {
const int n = 7;
for(i = 1; i<=n; i++)
for(j = 1; j<=n; j++) {
double s = 0.0;
for(k = 1; k<=n; k++)
s = s + a.m[i][k]*b.m[j][k];
c.m[i][j] = s;
}
} else {
const int n = lmax;
for(i = 1; i<=n; i++)
for(j = 1; j<=n; j++) {
double s = 0.0;
for(k = 1; k<=n; k++)
s = s + a.m[i][k]*b.m[j][k];
c.m[i][j] = s;
}
}
}
inline double transtrace_s(const float (*A)[8],const float (*B)[8]) const {
const int n = lmax;
double s = 0.0;
int i,j;
for(i = 0; i<n; i++)
for(j = 1; j<=n; j++)
s = s + A[i][j]*B[i][j];
return s;
}
inline double transtrace(const Matrix& a,const Matrix& b) const
{
int i,k;
double s = 0.0;
if(linalg.single)
return transtrace_s((const float (*)[8]) &a.m[1][0],(const float (*)[8]) &b.m[1][0]);
//printf("Calling transtrace... That is shit\n");
if(lmax == 5) {
const int n = 5;
for(i = 1; i<=n; i++)
for(k = 1; k<=n; k++)
s = s + a.m[i][k]*b.m[i][k];
} else if(lmax == 7) {
const int n = 7;
for(i = 1; i<=n; i++)
for(k = 1; k<=n; k++)
s = s + a.m[i][k]*b.m[i][k];
} else {
const int n = lmax;
for(i = 1; i<=n; i++)
for(k = 1; k<=n; k++)
s = s + a.m[i][k]*b.m[i][k];
}
return s;
}
double cutoff;
//double vpair[601];
//double ktan[601];
//double dvdvol[601];
//double delr;
//double rp,p1,al,r0,vc,vd,ve,pc,pd,pe;
double rmax;
double rcrit;
//double evol0, pvol0, pot_input_vol;
//double epsr, epsa;
int thrion;
int fourion;
//int mode;
double ddl[5];
int lmax, lang;
Matrix del0;
double anorm3, anorm4;
// Flag indicating whether volumetric pressure should be used.
// Volumetric pressure means that terms emanating from the
// derivative of the energy with respect to the potential atomic
// volume parameter is included.
int volpres_flag,nbody_flag;
potdata splinepot;
};
}
#endif
#endif
/* ----------------------------------------------------------------------
* Fast Model Generalized Pseudopotential Theory (MGPT) interatomic
* potential routine.
*
* Copyright (2015) Lawrence Livermore National Security, LLC.
* Produced at the Lawrence Livermore National Laboratory.
* Written by Tomas Oppelstrup (oppelstrup2@llnl.gov) and John Moriarty
* (moriarty2@llnl.gov)
* LLNL-CODE-674031 All rights reserved.
*
* This program is free software; you can redistribute it and/or modify it under
* the terms of the GNU General Public License (as published by the Free
* Software Foundation) version 2, dated June 1991.
*
* This program is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF MERCHANTABILITY
* or FITNESS FOR A PARTICULAR PURPOSE. See the terms and conditions of the
* GNU General Public License for more details.
*
* LLNL Preamble Notice
* A. This notice is required to be provided under our contract with the
* U.S. Department of Energy (DOE). This work was performed under the auspices
* of the DOE by Lawrence Livermore National Laboratory under Contract No.
* DE-AC52-07NA27344.
*
* B. Neither the United States Government nor Lawrence Livermore National
* Security, LLC nor any of their employees, makes any warranty, express or
* implied, or assumes any liability or responsibility for the accuracy,
* completeness, or usefulness of any information, apparatus, product, or
* process disclosed, or represents that its use would not infringe
* privately-owned rights.
*
* C. Also, reference herein to any specific commercial products, process,
* or services by trade name, trademark, manufacturer or otherwise does not
* necessarily constitute or imply its endorsement, recommendation, or
* favoring by the United States Government or Lawrence Livermore National
* Security, LLC. The views and opinions of authors expressed herein do not
* necessarily state or reflect those of the United States Government or
* Lawrence Livermore National Security, LLC, and shall not be used for
* advertising or product endorsement purposes.
------------------------------------------------------------------------- */

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