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pair_comb3.h
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pair_comb3.h
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/* -*- c++ -*- ----------------------------------------------------------
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(comb3,PairComb3)
#else
#ifndef LMP_PAIR_COMB3_H
#define LMP_PAIR_COMB3_H
#include "pair.h"
#include "my_page.h"
namespace LAMMPS_NS {
class PairComb3 : public Pair {
public:
PairComb3(class LAMMPS *);
virtual ~PairComb3();
virtual void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
void init_style();
double init_one(int, int);
double memory_usage();
virtual double combqeq(double *, int &);
double enegtot;
// general potential parameters
protected:
struct Param {
int ielement,jelement,kelement,powermint;
int ielementgp,jelementgp,kelementgp; //element group
int ang_flag,pcn_flag,rad_flag,tor_flag; //angle, coordination,radical, torsion flag
double lami,lambda,alfi,alpha1,alpha2,alpha3,beta;
double pcos6,pcos5,pcos4,pcos3,pcos2,pcos1,pcos0;
double gamma,powerm,powern,bigA,bigB1,bigB2,bigB3;
double bigd,bigr,cut,cutsq,c1,c2,c3,c4;
double p6p0,p6p1,p6p2,p6p3,p6p4,p6p5,p6p6;
double ptork1,ptork2;
double addrepr,addrep, vdwflag;
double QU,QL,DU,DL,Qo,dQ,aB,bB,nD,bD,qmin,qmax;
double chi,dj,dk,dl,dm,esm,cmn1,cmn2,pcmn1,pcmn2;
double coulcut, lcut, lcutsq;
double veps, vsig, pcna, pcnb, pcnc, pcnd, polz, curl, pcross;
double paaa, pbbb;
double curlcut1, curlcut2, curl0;
};
// general setups
int nelements; // # of unique elements
int ***elem2param; // mapping from element triplets to parameters
int *map; // mapping from atom types to elements
int nparams; // # of stored parameter sets
int maxparam; // max # of parameter sets
double PI,PI2,PI4,PIsq; // PIs
double cutmin; // min cutoff for all elements
double cutmax; // max cutoff for all elements
double precision; // tolerance for QEq convergence
char **elements; // names of unique elements
Param *params; // parameter set for an I-J-K interaction
int debug_eng1, debug_eng2, debug_fq; // logic controlling debugging outputs
int pack_flag;
// Short range neighbor list
void Short_neigh();
int pgsize, oneatom;
int *sht_num, **sht_first;
MyPage<int> *ipage;
// loop up tables and flags
int nmax, **intype;
int pol_flag, polar;
double *qf, **bbij, *charge, *NCo;
double *esm, **fafb, **dfafb, **ddfafb, **phin, **dphin, **erpaw;
double **vvdw, **vdvdw;
double **afb, **dafb;
double **dpl, bytes;
double *xcctmp, *xchtmp, *xcotmp;
// additional carbon parameters
int cflag;
int nsplpcn,nsplrad,nspltor;
int maxx,maxy,maxz,maxxc,maxyc,maxconj;
int maxxcn[4];
double vmaxxcn[4],dvmaxxcn[4];
int ntab;
double iin2[16][2],iin3[64][3];
double brad[4], btor[4], bbtor, ptorr;
double fi_tor[3], fj_tor[3], fk_tor[3], fl_tor[3];
double radtmp, fi_rad[3], fj_rad[3], fk_rad[3];
double ccutoff[6],ch_a[7];
//COMB3-v18 arrays for CHO
// We wanna dynamic arrays
// C angle arrays, size = ntab+1
double pang[20001];
double dpang[20001];
double ddpang[20001];
//coordination spline arrays
double pcn_grid[4][5][5][5];
double pcn_gridx[4][5][5][5];
double pcn_gridy[4][5][5][5];
double pcn_gridz[4][5][5][5];
double pcn_cubs[4][4][4][4][64];
//coordination spline arrays
double rad_grid[3][5][5][11];
double rad_gridx[3][5][5][11];
double rad_gridy[3][5][5][11];
double rad_gridz[3][5][5][11];
double rad_spl[3][4][4][10][64];
//torsion spline arrays
double tor_grid[1][5][5][11];
double tor_gridx[1][5][5][11];
double tor_gridy[1][5][5][11];
double tor_gridz[1][5][5][11];
double tor_spl[1][4][4][10][64];
// initialization functions
void allocate();
void read_lib();
void setup();
virtual void read_file(char *);
// cutoff functions
double comb_fc(double, Param *);
double comb_fc_d(double, Param *);
double comb_fc_curl(double, Param *);
double comb_fc_curl_d(double, Param *);
double comb_fccc(double);
double comb_fccc_d(double);
double comb_fcch(double);
double comb_fcch_d(double);
double comb_fccch(double);
double comb_fccch_d(double);
double comb_fcsw(double);
// short range terms
void attractive(Param *, Param *, Param *, double, double, double, double,
double, double, double, double *, double *, double *,
double *, double *, int, double);
virtual void comb_fa(double, Param *, Param *, double, double,
double &, double &);
virtual void repulsive(Param *, Param *,double, double &, int,
double &, double, double);
// bond order terms
double comb_bij(double, Param *, double, int, double);
double comb_gijk(double, Param *, double);
void comb_gijk_d(double, Param *, double, double &, double &);
double zeta(Param *, Param *, double, double, double *, double *, int, double);
void comb_bij_d(double, Param *, double, int, double &,
double &, double &, double &, double &, double &, double);
void coord(Param *, double, int, double &, double &,
double &, double &, double &, double);
void comb_zetaterm_d(double, double, double, double, double,
double *, double, double *, double, double *, double *,
double *, Param *, Param *, Param *, double);
void costheta_d(double *, double, double *, double,
double *, double *, double *);
void force_zeta(Param *, Param *, double, double, double, double &,
double &, double &, double &, double &, double &, double &,
double &, double &, double &, double &, double &, double &,
int, double &, double,double, int, int, int,
double , double , double);
void cntri_int(int, double, double, double, int, int, int,
double &, double &, double &, double &, Param *);
// Legendre polynomials
void selfp6p(Param *, Param *, double, double &, double &);
double ep6p(Param *, Param *, double, double, double *, double * ,double &);
void fp6p(Param *, Param *, double, double, double *, double *, double *,
double *, double *);
// long range q-dependent terms
double self(Param *, double);
void tables();
void potal_calc(double &, double &, double &);
void tri_point(double, int &, int &, int &, double &, double &,
double &);
void vdwaals(int,int,int,int,double,double,double,double,
double &, double &);
void direct(Param *, Param *, int,int,int,double,double,
double,double,double,double, double,double,double &,double &,
int, int);
void field(Param *, Param *,double,double,double,double &,double &);
int heaviside(double);
double switching(double);
double switching_d(double);
double chicut1, chicut2;
// radical terms
double rad_init(double, Param *, int, double &, double);
void rad_calc(double, Param *, Param *, double, double, int,
int, double, double);
void rad_int(int , double, double, double, int, int, int,
double &, double &, double &, double &);
void rad_forceik(Param *, double, double *, double, double);
void rad_force(Param *, double, double *, double);
// torsion terms
double bbtor1(int, Param *, Param *, double, double, double,
double *, double *, double *, double); //modified by TAO
void tor_calc(double, Param *, Param *, double, double, int,
int, double, double);
void tor_int(int , double, double, double, int, int, int,
double &, double &, double &, double &);
void tor_force(int, Param *, Param *, double, double, double,
double, double *, double *, double *); //modified by TAO
// charge force terms
double qfo_self(Param *, double);
void qfo_short(Param *, Param *, double, double, double,
double &, double &, int, int, int);
void qfo_direct(Param *, Param *, int, int, int, double,
double, double, double, double, double &, double &,
double, double, int, int);
void qfo_field(Param *, Param *,double,double ,double ,double &, double &);
void qfo_dipole(double, int, int, int, int, double, double *, double,
double, double, double &, double &, int, int);
void qsolve(double *);
// dipole - polarization terms
double dipole_self(Param *, int);
void dipole_init(Param *, Param *, double, double *, double,
int, int, int, double, double, double, double, double, int , int);
void dipole_calc(Param *, Param *, double, double, double, double, double,
int, int, int, double, double, double, double, double, int , int,
double &, double &, double *);
// communication functions
int pack_reverse_comm(int, int, double *);
void unpack_reverse_comm(int, int *, double *);
int pack_forward_comm(int , int *, double *, int, int *);
void unpack_forward_comm(int , int , double *);
// vector functions, inline for efficiency
inline double vec3_dot(double *x, double *y) {
return x[0]*y[0] + x[1]*y[1] + x[2]*y[2];
}
inline void vec3_add(double *x, double *y, double *z) {
z[0] = x[0]+y[0]; z[1] = x[1]+y[1]; z[2] = x[2]+y[2];
}
inline void vec3_scale(double k, double *x, double *y) {
y[0] = k*x[0]; y[1] = k*x[1]; y[2] = k*x[2];
}
inline void vec3_scaleadd(double k, double *x, double *y, double *z) {
z[0] = k*x[0]+y[0]; z[1] = k*x[1]+y[1]; z[2] = k*x[2]+y[2];
}
};
}
#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 COMB3 requires atom IDs
This is a requirement to use the COMB3 potential.
E: Pair style COMB3 requires newton pair on
See the newton command. This is a restriction to use the COMB3
potential.
E: Pair style COMB3 requires atom attribute q
Self-explanatory.
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 COMB3 lib.comb3 file
The COMB3 library file cannot be opened. Check that the path and name
are correct.
E: Cannot open COMB3 potential file %s
The specified COMB3 potential file cannot be opened. Check that the
path and name are correct.
E: Incorrect format in COMB3 potential file
Incorrect number of words per line in the potential file.
E: Illegal COMB3 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.
E: Neighbor list overflow, boost neigh_modify one
There are too many neighbors of a single atom. Use the neigh_modify
command to increase the max number of neighbors allowed for one atom.
You may also want to boost the page size.
E: Error in vdw spline: inner radius > outer radius
A pre-tabulated spline is invalid. Likely a problem with the
potential parameters.
*/

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