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restart2data.cpp
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restart2data.cpp
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/* -----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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.
------------------------------------------------------------------------ */
// Convert a LAMMPS binary restart file into an ASCII text data file
//
// Syntax: restart2data restart-file data-file (input-file)
// restart-file and data-file are mandatory
// input-file is optional
// if specified it will contain LAMMPS input script commands
// for mass and force field info
// only a few force field styles support this option
//
// this serial code must be compiled on a platform that can read the binary
// restart file since binary formats are not compatible across all platforms
// restart-file can have a '%' character to indicate a multiproc restart
// file as written by LAMMPS
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
#define MAX_GROUP 32
#define PI (4.0*atan(1.0))
// these must match settings in src/lmptype.h
// depending on whether you built LAMMPS with
// -DLAMMPS_SMALLBIG (the default), -DLAMMPS_BIGBIG, or -DLAMMPS_SMALLSMALL
#include "stdint.h"
#define __STDC_FORMAT_MACROS
#include "inttypes.h"
#ifndef PRId64
#define PRId64 "ld"
#endif
#if !defined(LAMMPS_SMALLSMALL) && !defined(LAMMPS_BIGBIG) && !defined(LAMMPS_SMALLBIG)
#define LAMMPS_SMALLBIG
#endif
#if defined(LAMMPS_SMALLBIG)
typedef int tagint;
typedef int64_t bigint;
#define BIGINT_FORMAT "%" PRId64
#define IMGMASK 1023
#define IMGMAX 512
#define IMGBITS 10
#define IMG2BITS 20
#elif defined(LAMMPS_SMALLSMALL)
typedef int tagint;
typedef int bigint;
#define BIGINT_FORMAT "%d"
#define IMGMASK 1023
#define IMGMAX 512
#define IMGBITS 10
#define IMG2BITS 20
#else /* LAMMPS_BIGBIG */
typedef int64_t tagint;
typedef int64_t bigint;
#define BIGINT_FORMAT "%" PRId64
#define IMGMASK 2097151
#define IMGMAX 1048576
#define IMGBITS 21
#define IMG2BITS 42
#endif
// same as write_restart.cpp
enum{VERSION,SMALLINT,TAGINT,BIGINT,
UNITS,NTIMESTEP,DIMENSION,NPROCS,PROCGRID_0,PROCGRID_1,PROCGRID_2,
NEWTON_PAIR,NEWTON_BOND,XPERIODIC,YPERIODIC,ZPERIODIC,
BOUNDARY_00,BOUNDARY_01,BOUNDARY_10,BOUNDARY_11,BOUNDARY_20,BOUNDARY_21,
ATOM_STYLE,NATOMS,NTYPES,
NBONDS,NBONDTYPES,BOND_PER_ATOM,
NANGLES,NANGLETYPES,ANGLE_PER_ATOM,
NDIHEDRALS,NDIHEDRALTYPES,DIHEDRAL_PER_ATOM,
NIMPROPERS,NIMPROPERTYPES,IMPROPER_PER_ATOM,
BOXLO_0,BOXHI_0,BOXLO_1,BOXHI_1,BOXLO_2,BOXHI_2,
SPECIAL_LJ_1,SPECIAL_LJ_2,SPECIAL_LJ_3,
SPECIAL_COUL_1,SPECIAL_COUL_2,SPECIAL_COUL_3,
XY,XZ,YZ};
enum{MASS};
enum{PAIR,BOND,ANGLE,DIHEDRAL,IMPROPER};
static const char * const cg_type_list[] =
{"none", "lj9_6", "lj12_4", "lj12_6"};
int swapflag;
// ---------------------------------------------------------------------
// Data class to hold problem
// ---------------------------------------------------------------------
class Data {
public:
// global settings
char *version;
int size_smallint,size_tagint,size_bigint;
bigint ntimestep;
int nprocs;
char *unit_style;
int dimension;
int px,py,pz;
int newton_pair,newton_bond;
int xperiodic,yperiodic,zperiodic;
int boundary[3][2];
char *atom_style;
int style_angle,style_atomic,style_bond,style_charge,style_dipole;
int style_ellipsoid,style_full,style_line,style_meso;
int style_molecular,style_peri,style_sphere;
int style_tri,style_wavepacket,style_hybrid;
bigint natoms;
bigint nellipsoids;
bigint nbonds,nangles,ndihedrals,nimpropers;
int ntypes,nbondtypes,nangletypes,ndihedraltypes,nimpropertypes;
int bond_per_atom,angle_per_atom,dihedral_per_atom,improper_per_atom;
int triclinic;
double xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz;
double special_lj[4],special_coul[4];
double cut_lj_global,cut_coul_global,kappa;
int offset_flag,mix_flag,tail_flag,ncoultablebits;
double tabinner;
// force fields
char *pair_style,*bond_style,*angle_style,*dihedral_style,*improper_style;
double *pair_born_A,*pair_born_rho,*pair_born_sigma;
double *pair_born_C,*pair_born_D;
double *pair_buck_A,*pair_buck_rho,*pair_buck_C;
double *pair_colloid_A12,*pair_colloid_sigma;
double *pair_colloid_d1,*pair_colloid_d2;
double *pair_dipole_epsilon,*pair_dipole_sigma;
double *pair_dpd_a0,*pair_dpd_gamma;
double *pair_charmm_epsilon,*pair_charmm_sigma;
double *pair_charmm_eps14,*pair_charmm_sigma14;
double *pair_class2_epsilon,*pair_class2_sigma;
double *pair_gb_epsilon,*pair_gb_sigma;
double *pair_gb_epsa,*pair_gb_epsb,*pair_gb_epsc;
double *pair_lj_epsilon,*pair_lj_sigma;
double *pair_gauss_hgauss,*pair_gauss_rmh,*pair_gauss_sigmah;
double **pair_cg_epsilon,**pair_cg_sigma;
int **pair_cg_cmm_type, **pair_setflag;
double **pair_cut_coul, **pair_cut_lj;
double *pair_ljexpand_epsilon,*pair_ljexpand_sigma,*pair_ljexpand_shift;
double *pair_ljgromacs_epsilon,*pair_ljgromacs_sigma;
double *pair_ljsmooth_epsilon,*pair_ljsmooth_sigma;
double *pair_morse_d0,*pair_morse_alpha,*pair_morse_r0;
double *pair_soft_A;
double *pair_yukawa_A;
double *bond_class2_r0,*bond_class2_k2,*bond_class2_k3,*bond_class2_k4;
double *bond_fene_k,*bond_fene_r0,*bond_fene_epsilon,*bond_fene_sigma;
double *bond_feneexpand_k,*bond_feneexpand_r0;
double *bond_feneexpand_epsilon,*bond_feneexpand_sigma;
double *bond_feneexpand_shift;
double *bond_harmonic_k,*bond_harmonic_r0;
double *bond_harmonicshift_umin,*bond_harmonicshift_r0,
*bond_harmonicshift_rc;
double *bond_harmonicshiftcut_umin,*bond_harmonicshiftcut_r0,
*bond_harmonicshiftcut_rc;
double *bond_morse_d0,*bond_morse_alpha,*bond_morse_r0;
double *bond_nonlinear_epsilon,*bond_nonlinear_r0,*bond_nonlinear_lamda;
double *bond_quartic_k,*bond_quartic_b1,*bond_quartic_b2;
double *bond_quartic_rc,*bond_quartic_u0;
double *angle_charmm_k,*angle_charmm_theta0;
double *angle_charmm_k_ub,*angle_charmm_r_ub;
double *angle_class2_theta0;
double *angle_class2_k2,*angle_class2_k3,*angle_class2_k4;
double *angle_class2_bb_k,*angle_class2_bb_r1,*angle_class2_bb_r2;
double *angle_class2_ba_k1,*angle_class2_ba_k2;
double *angle_class2_ba_r1,*angle_class2_ba_r2;
double *angle_cosine_k;
double *angle_cosine_squared_k,*angle_cosine_squared_theta0;
double *angle_harmonic_k,*angle_harmonic_theta0;
double *angle_cg_cmm_epsilon,*angle_cg_cmm_sigma;
double *angle_cosineshift_umin,*angle_cosineshift_sint,
*angle_cosineshift_cost,*angle_cosineshift_theta0;
double *angle_cosineshiftexp_umin,*angle_cosineshiftexp_a,
*angle_cosineshiftexp_sint,*angle_cosineshiftexp_cost,
*angle_cosineshiftexp_theta0;
int *angle_cg_cmm_type;
double *dihedral_charmm_k,*dihedral_charmm_weight;
int *dihedral_charmm_multiplicity,*dihedral_charmm_sign;
double *dihedral_class2_k1,*dihedral_class2_k2,*dihedral_class2_k3;
double *dihedral_class2_phi1,*dihedral_class2_phi2,*dihedral_class2_phi3;
double *dihedral_class2_mbt_f1,*dihedral_class2_mbt_f2;
double *dihedral_class2_mbt_f3,*dihedral_class2_mbt_r0;
double *dihedral_class2_ebt_f1_1,*dihedral_class2_ebt_f2_1;
double *dihedral_class2_ebt_f3_1,*dihedral_class2_ebt_r0_1;
double *dihedral_class2_ebt_f1_2,*dihedral_class2_ebt_f2_2;
double *dihedral_class2_ebt_f3_2,*dihedral_class2_ebt_r0_2;
double *dihedral_class2_at_f1_1,*dihedral_class2_at_f2_1;
double *dihedral_class2_at_f3_1,*dihedral_class2_at_theta0_1;
double *dihedral_class2_at_f1_2,*dihedral_class2_at_f2_2;
double *dihedral_class2_at_f3_2,*dihedral_class2_at_theta0_2;
double *dihedral_class2_aat_k;
double *dihedral_class2_aat_theta0_1,*dihedral_class2_aat_theta0_2;
double *dihedral_class2_bb13_k;
double *dihedral_class2_bb13_r10,*dihedral_class2_bb13_r30;
double *dihedral_harmonic_k;
int *dihedral_harmonic_multiplicity,*dihedral_harmonic_sign;
double *dihedral_helix_aphi,*dihedral_helix_bphi,*dihedral_helix_cphi;
double *dihedral_multi_a1,*dihedral_multi_a2,*dihedral_multi_a3;
double *dihedral_multi_a4,*dihedral_multi_a5;
double *dihedral_opls_k1,*dihedral_opls_k2;
double *dihedral_opls_k3,*dihedral_opls_k4;
double *dihedral_cosineshiftexp_umin, *dihedral_cosineshiftexp_a,
*dihedral_cosineshiftexp_sint,*dihedral_cosineshiftexp_cost,
*dihedral_cosineshiftexp_theta;
double *improper_class2_k0,*improper_class2_chi0;
double *improper_class2_aa_k1,*improper_class2_aa_k2,*improper_class2_aa_k3;
double *improper_class2_aa_theta0_1,*improper_class2_aa_theta0_2;
double *improper_class2_aa_theta0_3;
double *improper_cvff_k;
int *improper_cvff_sign,*improper_cvff_multiplicity;
double *improper_harmonic_k,*improper_harmonic_chi;
// atom quantities
bigint iatoms,ibonds,iangles,idihedrals,iimpropers;
double *mass;
double *x,*y,*z,*vx,*vy,*vz;
double *omegax,*omegay,*omegaz;
int *tag;
int *type,*mask;
tagint *image;
int *molecule;
double *q,*mux,*muy,*muz,*mul,*radius,*density,*vfrac,*rmass;
double *s0,*x0x,*x0y,*x0z;
double *shapex,*shapey,*shapez;
double *quatw,*quati,*quatj,*quatk,*angmomx,*angmomy,*angmomz;
int *ellipsoid;
int *bond_type,*angle_type,*dihedral_type,*improper_type;
int *bond_atom1,*bond_atom2;
int *angle_atom1,*angle_atom2,*angle_atom3;
int *dihedral_atom1,*dihedral_atom2,*dihedral_atom3,*dihedral_atom4;
int *improper_atom1,*improper_atom2,*improper_atom3,*improper_atom4;
// functions
Data();
void stats();
void write(FILE *, FILE *, int, int);
void write_atom_angle(FILE *, int, int, int, int);
void write_atom_atomic(FILE *, int, int, int, int);
void write_atom_bond(FILE *, int, int, int, int);
void write_atom_charge(FILE *, int, int, int, int);
void write_atom_dipole(FILE *, int, int, int, int);
void write_atom_ellipsoid(FILE *, int, int, int, int);
void write_atom_full(FILE *, int, int, int, int);
void write_atom_line(FILE *, int, int, int, int);
void write_atom_meso(FILE *, int, int, int, int);
void write_atom_molecular(FILE *, int, int, int, int);
void write_atom_peri(FILE *, int, int, int, int);
void write_atom_sphere(FILE *, int, int, int, int);
void write_atom_tri(FILE *, int, int, int, int);
void write_atom_wavepacket(FILE *, int, int, int, int);
void write_atom_angle_extra(FILE *, int);
void write_atom_atomic_extra(FILE *, int);
void write_atom_bond_extra(FILE *, int);
void write_atom_charge_extra(FILE *, int);
void write_atom_dipole_extra(FILE *, int);
void write_atom_ellipsoid_extra(FILE *, int);
void write_atom_full_extra(FILE *, int);
void write_atom_line_extra(FILE *, int);
void write_atom_meso_extra(FILE *, int);
void write_atom_molecular_extra(FILE *, int);
void write_atom_peri_extra(FILE *, int);
void write_atom_sphere_extra(FILE *, int);
void write_atom_tri_extra(FILE *, int);
void write_atom_wavepacket_extra(FILE *, int);
void write_vel_angle(FILE *, int);
void write_vel_atomic(FILE *, int);
void write_vel_bond(FILE *, int);
void write_vel_charge(FILE *, int);
void write_vel_dipole(FILE *, int);
void write_vel_ellipsoid(FILE *, int);
void write_vel_full(FILE *, int);
void write_vel_line(FILE *, int);
void write_vel_meso(FILE *, int);
void write_vel_molecular(FILE *, int);
void write_vel_peri(FILE *, int);
void write_vel_sphere(FILE *, int);
void write_vel_tri(FILE *, int);
void write_vel_wavepacket(FILE *, int);
void write_vel_angle_extra(FILE *, int);
void write_vel_atomic_extra(FILE *, int);
void write_vel_bond_extra(FILE *, int);
void write_vel_charge_extra(FILE *, int);
void write_vel_dipole_extra(FILE *, int);
void write_vel_ellipsoid_extra(FILE *, int);
void write_vel_full_extra(FILE *, int);
void write_vel_line_extra(FILE *, int);
void write_vel_meso_extra(FILE *, int);
void write_vel_molecular_extra(FILE *, int);
void write_vel_peri_extra(FILE *, int);
void write_vel_sphere_extra(FILE *, int);
void write_vel_tri_extra(FILE *, int);
void write_vel_wavepacket_extra(FILE *, int);
};
// ---------------------------------------------------------------------
// function prototypes
// ---------------------------------------------------------------------
void header(FILE *, Data &);
void set_style(char *, Data &, int);
void groups(FILE *);
void type_arrays(FILE *, Data &);
void force_fields(FILE *, Data &);
void modify(FILE *);
void pair(FILE *fp, Data &data, char *style, int flag);
void bond(FILE *fp, Data &data);
void angle(FILE *fp, Data &data);
void dihedral(FILE *fp, Data &data);
void improper(FILE *fp, Data &data);
int atom(double *, Data &data);
void allocate_angle(Data &data);
void allocate_atomic(Data &data);
void allocate_bond(Data &data);
void allocate_charge(Data &data);
void allocate_dipole(Data &data);
void allocate_ellipsoid(Data &data);
void allocate_full(Data &data);
void allocate_line(Data &data);
void allocate_meso(Data &data);
void allocate_molecular(Data &data);
void allocate_peri(Data &data);
void allocate_sphere(Data &data);
void allocate_tri(Data &data);
void allocate_wavepacket(Data &data);
int atom_angle(double *, Data &, int);
int atom_atomic(double *, Data &, int);
int atom_bond(double *, Data &, int);
int atom_charge(double *, Data &, int);
int atom_dipole(double *, Data &, int);
int atom_ellipsoid(double *, Data &, int);
int atom_full(double *, Data &, int);
int atom_line(double *, Data &, int);
int atom_meso(double *, Data &, int);
int atom_molecular(double *, Data &, int);
int atom_peri(double *, Data &, int);
int atom_sphere(double *, Data &, int);
int atom_tri(double *, Data &, int);
int atom_wavepacket(double *, Data &, int);
void strip_suffix(char *);
void nread_int(int *buf, int n, FILE *fp);
void nread_double(double *buf, int n, FILE *fp);
int read_int(FILE *fp);
double read_double(FILE *fp);
char *read_char(FILE *fp);
bigint read_bigint(FILE *fp);
int autodetect(FILE **, char *);
static void helpmsg(int exitval)
{
printf("Syntax: restart2data (switch1 switch2 ...) "
"restart-file data-file (input-file)\n");
printf(" 'restart-file' and 'data-file' are mandatory\n");
printf(" 'input-file' is optional\n");
printf(" If specified, it will contain LAMMPS input script\n");
printf(" commands for mass and force field info.\n");
printf(" Only a few force field styles support this option.\n");
printf(" Switches are optional. Supported switches:\n");
printf(" -h print this message\n");
printf(" -nc don't write out coefficients\n");
printf(" -nv don't write out velocities\n");
exit(exitval);
}
// ---------------------------------------------------------------------
// main program
// ---------------------------------------------------------------------
int main (int narg, char **arg)
{
// process command-line args
if (narg < 2) helpmsg(1);
int iarg,write_coeffs,write_vels;
char *restartfile, *datafile, *inputfile;
write_coeffs = write_vels = 1;
restartfile = datafile = inputfile = NULL;
for (iarg = 1; iarg < narg; ++iarg) {
if (strcmp(arg[iarg],"-h") == 0) {
helpmsg(0);
} else if (strcmp(arg[iarg],"-nc") == 0) {
write_coeffs = 0;
} else if (strcmp(arg[iarg],"-nv") == 0) {
write_vels = 0;
} else if (!restartfile) {
restartfile = arg[iarg];
} else if (!datafile) {
datafile = arg[iarg];
} else if (!inputfile) {
inputfile = arg[iarg];
}
}
if (!restartfile || !datafile) helpmsg(2);
// if restart file contains '%', file = filename with % replaced by "base"
// else file = single file
// open single restart file or base file for multiproc case
// auto-detect whether byte swapping needs to be done as file is read
printf("Reading restart file ...\n");
char *ptr;
FILE *fp;
int multiproc = 0;
if ( (ptr = strchr(restartfile,'%')) ) {
multiproc = 1;
char *basefile = new char[strlen(restartfile) + 16];
*ptr = '\0';
sprintf(basefile,"%s%s%s",restartfile,"base",ptr+1);
fp = fopen(basefile,"rb");
if (fp == NULL) {
printf("ERROR: Cannot open restart file %s\n",basefile);
return 1;
}
swapflag = autodetect(&fp,basefile);
} else {
fp = fopen(restartfile,"rb");
if (fp == NULL) {
printf("ERROR: Cannot open restart file %s\n",restartfile);
return 1;
}
swapflag = autodetect(&fp,restartfile);
}
// read beginning of restart file
Data data;
header(fp,data);
if (data.size_smallint != sizeof(int) ||
data.size_tagint != sizeof(tagint) ||
data.size_bigint != sizeof(bigint)) {
printf("ERROR: Data type sizes in restart file "
"are incompatible with restart2data.cpp\n");
return 1;
}
groups(fp);
type_arrays(fp,data);
force_fields(fp,data);
modify(fp);
// read atoms from single or multiple restart files
double *buf = NULL;
int n,m;
int maxbuf = 0;
data.iatoms = data.ibonds = data.iangles =
data.idihedrals = data.iimpropers = 0;
for (int iproc = 0; iproc < data.nprocs; iproc++) {
if (multiproc) {
fclose(fp);
char *procfile;
sprintf(procfile,"%s%d%s",restartfile,iproc,ptr+1);
fp = fopen(procfile,"rb");
if (fp == NULL) {
printf("ERROR: Cannot open restart file %s\n",procfile);
return 1;
}
}
n = read_int(fp);
if (n > maxbuf) {
maxbuf = n;
delete [] buf;
buf = new double[maxbuf];
}
nread_double(buf,n,fp);
m = 0;
while (m < n) m += atom(&buf[m],data);
}
fclose(fp);
// print out stats
data.stats();
// write out data file and no input file
if (!inputfile) {
printf("Writing data file ...\n");
fp = fopen(datafile,"w");
if (fp == NULL) {
printf("ERROR: Cannot open data file %s\n",datafile);
return 1;
}
data.write(fp,NULL,write_coeffs,write_vels);
fclose(fp);
// write out data file and input file
} else {
printf("Writing data file ...\n");
fp = fopen(datafile,"w");
if (fp == NULL) {
printf("ERROR: Cannot open data file %s\n",datafile);
return 1;
}
printf("Writing input file ...\n");
FILE *fp2 = fopen(inputfile,"w");
if (fp2 == NULL) {
printf("ERROR: Cannot open input file %s\n",inputfile);
fclose(fp);
return 1;
}
data.write(fp,fp2,write_coeffs,write_vels);
fclose(fp);
fclose(fp2);
}
return 0;
}
// ---------------------------------------------------------------------
// read header of restart file
// ---------------------------------------------------------------------
void header(FILE *fp, Data &data)
{
const char *version = "23 July 2013-ICMS";
data.triclinic = 0;
int flag;
flag = read_int(fp);
while (flag >= 0) {
if (flag == VERSION) {
data.version = read_char(fp);
if (strcmp(version,data.version) != 0) {
const char *str =
"Restart file version does not match restart2data version";
printf("WARNING %s\n",str);
printf(" restart2data version = %s\n",version);
}
}
else if (flag == SMALLINT) data.size_smallint = read_int(fp);
else if (flag == TAGINT) data.size_tagint = read_int(fp);
else if (flag == BIGINT) data.size_bigint = read_int(fp);
else if (flag == UNITS) data.unit_style = read_char(fp);
else if (flag == NTIMESTEP) data.ntimestep = read_bigint(fp);
else if (flag == DIMENSION) data.dimension = read_int(fp);
else if (flag == NPROCS) data.nprocs = read_int(fp);
else if (flag == PROCGRID_0) data.px = read_int(fp);
else if (flag == PROCGRID_1) data.py = read_int(fp);
else if (flag == PROCGRID_2) data.pz = read_int(fp);
else if (flag == NEWTON_PAIR) data.newton_pair = read_int(fp);
else if (flag == NEWTON_BOND) data.newton_bond = read_int(fp);
else if (flag == XPERIODIC) data.xperiodic = read_int(fp);
else if (flag == YPERIODIC) data.yperiodic = read_int(fp);
else if (flag == ZPERIODIC) data.zperiodic = read_int(fp);
else if (flag == BOUNDARY_00) data.boundary[0][0] = read_int(fp);
else if (flag == BOUNDARY_01) data.boundary[0][1] = read_int(fp);
else if (flag == BOUNDARY_10) data.boundary[1][0] = read_int(fp);
else if (flag == BOUNDARY_11) data.boundary[1][1] = read_int(fp);
else if (flag == BOUNDARY_20) data.boundary[2][0] = read_int(fp);
else if (flag == BOUNDARY_21) data.boundary[2][1] = read_int(fp);
// if atom_style = hybrid:
// set data_style_hybrid to # of sub-styles
// read additional sub-class arguments
// set sub-styles to 1 to N
else if (flag == ATOM_STYLE) {
data.style_angle = data.style_atomic = data.style_bond =
data.style_charge = data.style_dipole = data.style_ellipsoid =
data.style_full = data.style_line = data.style_meso =
data.style_molecular = data.style_peri = data.style_sphere =
data.style_tri = data.style_wavepacket = data.style_hybrid = 0;
data.atom_style = read_char(fp);
strip_suffix(data.atom_style);
set_style(data.atom_style,data,1);
if (strcmp(data.atom_style,"hybrid") == 0) {
int nwords = read_int(fp);
set_style(data.atom_style,data,nwords);
char *substyle;
for (int i = 1; i <= nwords; i++) {
substyle = read_char(fp);
strip_suffix(substyle);
set_style(substyle,data,i);
}
}
}
else if (flag == NATOMS) data.natoms = read_bigint(fp);
else if (flag == NTYPES) data.ntypes = read_int(fp);
else if (flag == NBONDS) data.nbonds = read_bigint(fp);
else if (flag == NBONDTYPES) data.nbondtypes = read_int(fp);
else if (flag == BOND_PER_ATOM) data.bond_per_atom = read_int(fp);
else if (flag == NANGLES) data.nangles = read_bigint(fp);
else if (flag == NANGLETYPES) data.nangletypes = read_int(fp);
else if (flag == ANGLE_PER_ATOM) data.angle_per_atom = read_int(fp);
else if (flag == NDIHEDRALS) data.ndihedrals = read_bigint(fp);
else if (flag == NDIHEDRALTYPES) data.ndihedraltypes = read_int(fp);
else if (flag == DIHEDRAL_PER_ATOM) data.dihedral_per_atom = read_int(fp);
else if (flag == NIMPROPERS) data.nimpropers = read_bigint(fp);
else if (flag == NIMPROPERTYPES) data.nimpropertypes = read_int(fp);
else if (flag == IMPROPER_PER_ATOM) data.improper_per_atom = read_int(fp);
else if (flag == BOXLO_0) data.xlo = read_double(fp);
else if (flag == BOXHI_0) data.xhi = read_double(fp);
else if (flag == BOXLO_1) data.ylo = read_double(fp);
else if (flag == BOXHI_1) data.yhi = read_double(fp);
else if (flag == BOXLO_2) data.zlo = read_double(fp);
else if (flag == BOXHI_2) data.zhi = read_double(fp);
else if (flag == SPECIAL_LJ_1) data.special_lj[1] = read_double(fp);
else if (flag == SPECIAL_LJ_2) data.special_lj[2] = read_double(fp);
else if (flag == SPECIAL_LJ_3) data.special_lj[3] = read_double(fp);
else if (flag == SPECIAL_COUL_1) data.special_coul[1] = read_double(fp);
else if (flag == SPECIAL_COUL_2) data.special_coul[2] = read_double(fp);
else if (flag == SPECIAL_COUL_3) data.special_coul[3] = read_double(fp);
else if (flag == XY) {
data.triclinic = 1;
data.xy = read_double(fp);
} else if (flag == XZ) {
data.triclinic = 1;
data.xz = read_double(fp);
} else if (flag == YZ) {
data.triclinic = 1;
data.yz = read_double(fp);
} else {
printf("ERROR: Invalid flag in header section of restart file %d\n",
flag);
exit(1);
}
flag = read_int(fp);
}
}
// ---------------------------------------------------------------------
// set atom style to flag
// ---------------------------------------------------------------------
void set_style(char *name, Data &data, int flag)
{
if (strcmp(name,"angle") == 0) data.style_angle = flag;
else if (strcmp(name,"atomic") == 0) data.style_atomic = flag;
else if (strcmp(name,"bond") == 0) data.style_bond = flag;
else if (strcmp(name,"charge") == 0) data.style_charge = flag;
else if (strcmp(name,"dipole") == 0) data.style_dipole = flag;
else if (strcmp(name,"ellipsoid") == 0) data.style_ellipsoid = flag;
else if (strcmp(name,"full") == 0) data.style_full = flag;
else if (strcmp(name,"line") == 0) data.style_line = flag;
else if (strcmp(name,"meso") == 0) data.style_meso = flag;
else if (strcmp(name,"molecular") == 0) data.style_molecular = flag;
else if (strcmp(name,"peri") == 0) data.style_peri = flag;
else if (strcmp(name,"sphere") == 0) data.style_sphere = flag;
else if (strcmp(name,"tri") == 0) data.style_tri = flag;
else if (strcmp(name,"wavepacket") == 0) data.style_wavepacket = flag;
else if (strcmp(name,"hybrid") == 0) data.style_hybrid = flag;
else {
printf("ERROR: Unknown atom style %s\n",name);
exit(1);
}
}
// ---------------------------------------------------------------------
// read group info from restart file, just ignore it
// ---------------------------------------------------------------------
void groups(FILE *fp)
{
int ngroup = read_int(fp);
char *name;
// use count to not change restart format with deleted groups
// remove this on next major release
int count = 0;
for (int i = 0; i < MAX_GROUP; i++) {
name = read_char(fp);
if (name) {
delete [] name;
count++;
}
if (count == ngroup) break;
}
}
// ---------------------------------------------------------------------
// read type arrays from restart file
// ---------------------------------------------------------------------
void type_arrays(FILE *fp, Data &data)
{
data.mass = NULL;
int flag;
flag = read_int(fp);
while (flag >= 0) {
if (flag == MASS) {
data.mass = new double[data.ntypes+1];
nread_double(&data.mass[1],data.ntypes,fp);
} else {
printf("ERROR: Invalid flag in type arrays section of restart file %d\n",
flag);
exit(1);
}
flag = read_int(fp);
}
}
// ---------------------------------------------------------------------
// read force-field info from restart file
// ---------------------------------------------------------------------
void force_fields(FILE *fp, Data &data)
{
data.pair_style = data.bond_style = data.angle_style =
data.dihedral_style = data.improper_style = NULL;
int flag;
flag = read_int(fp);
while (flag >= 0) {
if (flag == PAIR) {
data.pair_style = read_char(fp);
strip_suffix(data.pair_style);
pair(fp,data,data.pair_style,1);
} else if (flag == BOND) {
data.bond_style = read_char(fp);
strip_suffix(data.bond_style);
bond(fp,data);
} else if (flag == ANGLE) {
data.angle_style = read_char(fp);
strip_suffix(data.angle_style);
angle(fp,data);
} else if (flag == DIHEDRAL) {
data.dihedral_style = read_char(fp);
strip_suffix(data.dihedral_style);
dihedral(fp,data);
} else if (flag == IMPROPER) {
data.improper_style = read_char(fp);
strip_suffix(data.improper_style);
improper(fp,data);
} else {
printf("ERROR: Invalid flag in force fields section of restart file %d\n",
flag);
exit(1);
}
flag = read_int(fp);
}
}
// ---------------------------------------------------------------------
// read fix info from restart file, just ignore it
// ---------------------------------------------------------------------
void modify(FILE *fp)
{
char *buf;
int n;
// nfix = # of fix entries with state
int nfix = read_int(fp);
// read each entry with id string, style string, chunk of data
for (int i = 0; i < nfix; i++) {
buf = read_char(fp); delete [] buf;
buf = read_char(fp); delete [] buf;
buf = read_char(fp); delete [] buf;
}
// nfix = # of fix entries with peratom info
int nfix_peratom = read_int(fp);
// read each entry with id string, style string, maxsize of one atom data
for (int i = 0; i < nfix_peratom; i++) {
buf = read_char(fp); delete [] buf;
buf = read_char(fp); delete [] buf;
n = read_int(fp);
}
}
// ---------------------------------------------------------------------
// read atom info from restart file and store in data struct
// ---------------------------------------------------------------------
int atom(double *buf, Data &data)
{
// allocate per-atom arrays
if (data.iatoms == 0) {
// common to all atom styles
data.x = new double[data.natoms];
data.y = new double[data.natoms];
data.z = new double[data.natoms];
data.tag = new int[data.natoms];
data.type = new int[data.natoms];
data.mask = new int[data.natoms];
data.image = new tagint[data.natoms];
data.vx = new double[data.natoms];
data.vy = new double[data.natoms];
data.vz = new double[data.natoms];
// style-specific arrays
// don't worry about re-allocating if style = hybrid
if (data.style_angle) allocate_angle(data);
if (data.style_atomic) allocate_atomic(data);
if (data.style_bond) allocate_bond(data);
if (data.style_charge) allocate_charge(data);
if (data.style_dipole) allocate_dipole(data);
if (data.style_ellipsoid) allocate_ellipsoid(data);
if (data.style_full) allocate_full(data);
if (data.style_line) allocate_line(data);
if (data.style_meso) allocate_meso(data);
if (data.style_molecular) allocate_molecular(data);
if (data.style_peri) allocate_peri(data);
if (data.style_sphere) allocate_sphere(data);
if (data.style_tri) allocate_tri(data);
if (data.style_wavepacket) allocate_wavepacket(data);
}
// read atom quantities from buf
// if hybrid, loop over all sub-styles in order listed
// if hybrid, loop index k will match style setting to insure correct order
int nloop = 1;
if (data.style_hybrid) nloop = data.style_hybrid;
int iatoms = data.iatoms;
int m = 0;
for (int k = 1; k <= nloop; k++) {
if (k == data.style_angle) m += atom_angle(&buf[m],data,iatoms);
if (k == data.style_atomic) m += atom_atomic(&buf[m],data,iatoms);
if (k == data.style_bond) m += atom_bond(&buf[m],data,iatoms);
if (k == data.style_charge) m += atom_charge(&buf[m],data,iatoms);
if (k == data.style_dipole) m += atom_dipole(&buf[m],data,iatoms);
if (k == data.style_ellipsoid) m += atom_ellipsoid(&buf[m],data,iatoms);
if (k == data.style_full) m += atom_full(&buf[m],data,iatoms);
if (k == data.style_line) m += atom_line(&buf[m],data,iatoms);
if (k == data.style_meso) m += atom_meso(&buf[m],data,iatoms);
if (k == data.style_molecular) m += atom_molecular(&buf[m],data,iatoms);
if (k == data.style_peri) m += atom_peri(&buf[m],data,iatoms);
if (k == data.style_sphere) m += atom_sphere(&buf[m],data,iatoms);
if (k == data.style_tri) m += atom_tri(&buf[m],data,iatoms);
if (k == data.style_wavepacket) m += atom_wavepacket(&buf[m],data,iatoms);
}
data.iatoms++;
m = static_cast<int> (buf[0]);
return m;
}
// ---------------------------------------------------------------------
// read one atom's info from buffer
// one routine per atom style
// skip broken bonds, angles, etc
// ---------------------------------------------------------------------
int atom_angle(double *buf, Data &data, int iatoms)
{
int type,atom1,atom2,atom3;
int m = 1;
data.x[iatoms] = buf[m++];
data.y[iatoms] = buf[m++];
data.z[iatoms] = buf[m++];
data.tag[iatoms] = static_cast<int> (buf[m++]);
data.type[iatoms] = static_cast<int> (buf[m++]);
data.mask[iatoms] = static_cast<int> (buf[m++]);
data.image[iatoms] = *((tagint *) &buf[m++]);
data.vx[iatoms] = buf[m++];
data.vy[iatoms] = buf[m++];
data.vz[iatoms] = buf[m++];
data.molecule[iatoms] = static_cast<int> (buf[m++]);
int n = static_cast<int> (buf[m++]);
for (int k = 0; k < n; k++) {
type = static_cast<int> (buf[m++]);
atom1 = static_cast<int> (buf[m++]);
if ((type != 0) && (data.newton_bond || (data.tag[iatoms] < atom1))) {
data.bond_type[data.ibonds] = type;
data.bond_atom1[data.ibonds] = data.tag[iatoms];
data.bond_atom2[data.ibonds] = atom1;
data.ibonds++;
}
}
n = static_cast<int> (buf[m++]);
for (int k = 0; k < n; k++) {
type = static_cast<int> (buf[m++]);
atom1 = static_cast<int> (buf[m++]);
atom2 = static_cast<int> (buf[m++]);
atom3 = static_cast<int> (buf[m++]);
if ((type != 0) && (data.newton_bond || (data.tag[iatoms] == atom2))) {
data.angle_type[data.iangles] = type;
data.angle_atom1[data.iangles] = atom1;
data.angle_atom2[data.iangles] = atom2;
data.angle_atom3[data.iangles] = atom3;
data.iangles++;
}
}
return m;
}
int atom_atomic(double *buf, Data &data, int iatoms)
{
int m = 1;
data.x[iatoms] = buf[m++];
data.y[iatoms] = buf[m++];
data.z[iatoms] = buf[m++];
data.tag[iatoms] = static_cast<int> (buf[m++]);
data.type[iatoms] = static_cast<int> (buf[m++]);
data.mask[iatoms] = static_cast<int> (buf[m++]);
data.image[iatoms] = *((tagint *) &buf[m++]);
data.vx[iatoms] = buf[m++];
data.vy[iatoms] = buf[m++];
data.vz[iatoms] = buf[m++];
return m;
}
int atom_bond(double *buf, Data &data, int iatoms)
{
int type,atom1;
int m = 1;
data.x[iatoms] = buf[m++];
data.y[iatoms] = buf[m++];
data.z[iatoms] = buf[m++];
data.tag[iatoms] = static_cast<int> (buf[m++]);
data.type[iatoms] = static_cast<int> (buf[m++]);
data.mask[iatoms] = static_cast<int> (buf[m++]);
data.image[iatoms] = *((tagint *) &buf[m++]);
data.vx[iatoms] = buf[m++];
data.vy[iatoms] = buf[m++];
data.vz[iatoms] = buf[m++];
data.molecule[iatoms] = static_cast<int> (buf[m++]);
int n = static_cast<int> (buf[m++]);
for (int k = 0; k < n; k++) {
type = static_cast<int> (buf[m++]);
atom1 = static_cast<int> (buf[m++]);
if ((type != 0) && (data.newton_bond || (data.tag[iatoms] < atom1))) {
data.bond_type[data.ibonds] = type;
data.bond_atom1[data.ibonds] = data.tag[iatoms];
data.bond_atom2[data.ibonds] = atom1;
data.ibonds++;
}
}
return m;
}
int atom_charge(double *buf, Data &data, int iatoms)
{
int m = 1;
data.x[iatoms] = buf[m++];
data.y[iatoms] = buf[m++];
data.z[iatoms] = buf[m++];
data.tag[iatoms] = static_cast<int> (buf[m++]);
data.type[iatoms] = static_cast<int> (buf[m++]);
data.mask[iatoms] = static_cast<int> (buf[m++]);
data.image[iatoms] = *((tagint *) &buf[m++]);
data.vx[iatoms] = buf[m++];
data.vy[iatoms] = buf[m++];
data.vz[iatoms] = buf[m++];
data.q[iatoms] = buf[m++];
return m;
}
int atom_dipole(double *buf, Data &data, int iatoms)
{
int m = 1;
data.x[iatoms] = buf[m++];
data.y[iatoms] = buf[m++];
data.z[iatoms] = buf[m++];
data.tag[iatoms] = static_cast<int> (buf[m++]);
data.type[iatoms] = static_cast<int> (buf[m++]);
data.mask[iatoms] = static_cast<int> (buf[m++]);
data.image[iatoms] = *((tagint *) &buf[m++]);
data.vx[iatoms] = buf[m++];
data.vy[iatoms] = buf[m++];
data.vz[iatoms] = buf[m++];
data.q[iatoms] = buf[m++];
data.mux[iatoms] = buf[m++];
data.muy[iatoms] = buf[m++];
data.muz[iatoms] = buf[m++];
data.mul[iatoms] = buf[m++];
return m;
}
int atom_ellipsoid(double *buf, Data &data, int iatoms)
{
int m = 1;
data.x[iatoms] = buf[m++];
data.y[iatoms] = buf[m++];
data.z[iatoms] = buf[m++];
data.tag[iatoms] = static_cast<int> (buf[m++]);
data.type[iatoms] = static_cast<int> (buf[m++]);
data.mask[iatoms] = static_cast<int> (buf[m++]);
data.image[iatoms] = *((tagint *) &buf[m++]);
data.vx[iatoms] = buf[m++];
data.vy[iatoms] = buf[m++];
data.vz[iatoms] = buf[m++];
data.rmass[iatoms] = buf[m++];
data.angmomx[iatoms] = buf[m++];
data.angmomy[iatoms] = buf[m++];
data.angmomz[iatoms] = buf[m++];
data.ellipsoid[iatoms] = static_cast<int> (buf[m++]);
if (data.ellipsoid[iatoms]) {
data.nellipsoids++;
data.shapex[iatoms] = buf[m++];
data.shapey[iatoms] = buf[m++];
data.shapez[iatoms] = buf[m++];
data.quatw[iatoms] = buf[m++];
data.quati[iatoms] = buf[m++];
data.quatj[iatoms] = buf[m++];
data.quatk[iatoms] = buf[m++];
data.density[iatoms] = data.rmass[iatoms] /
(4.0*PI/3.0 *
data.shapex[iatoms]*data.shapey[iatoms]*data.shapez[iatoms]);
} else data.density[iatoms] = data.rmass[iatoms];
return m;
}
int atom_full(double *buf, Data &data, int iatoms)
{
int type,atom1,atom2,atom3,atom4;
int m = 1;
data.x[iatoms] = buf[m++];
data.y[iatoms] = buf[m++];
data.z[iatoms] = buf[m++];
data.tag[iatoms] = static_cast<int> (buf[m++]);
data.type[iatoms] = static_cast<int> (buf[m++]);
data.mask[iatoms] = static_cast<int> (buf[m++]);
data.image[iatoms] = *((tagint *) &buf[m++]);
data.vx[iatoms] = buf[m++];
data.vy[iatoms] = buf[m++];
data.vz[iatoms] = buf[m++];
data.q[iatoms] = buf[m++];
data.molecule[iatoms] = static_cast<int> (buf[m++]);
int n = static_cast<int> (buf[m++]);
for (int k = 0; k < n; k++) {
type = static_cast<int> (buf[m++]);
atom1 = static_cast<int> (buf[m++]);
if ((type != 0) && (data.newton_bond || (data.tag[iatoms] < atom1))) {
data.bond_type[data.ibonds] = type;
data.bond_atom1[data.ibonds] = data.tag[iatoms];
data.bond_atom2[data.ibonds] = atom1;
data.ibonds++;
}
}
n = static_cast<int> (buf[m++]);
for (int k = 0; k < n; k++) {
type = static_cast<int> (buf[m++]);
atom1 = static_cast<int> (buf[m++]);
atom2 = static_cast<int> (buf[m++]);
atom3 = static_cast<int> (buf[m++]);
if ((type != 0) && (data.newton_bond || (data.tag[iatoms] == atom2))) {
data.angle_type[data.iangles] = type;
data.angle_atom1[data.iangles] = atom1;
data.angle_atom2[data.iangles] = atom2;
data.angle_atom3[data.iangles] = atom3;
data.iangles++;
}
}
n = static_cast<int> (buf[m++]);
for (int k = 0; k < n; k++) {
type = static_cast<int> (buf[m++]);
atom1 = static_cast<int> (buf[m++]);
atom2 = static_cast<int> (buf[m++]);
atom3 = static_cast<int> (buf[m++]);
atom4 = static_cast<int> (buf[m++]);
if ((type != 0) && (data.newton_bond || (data.tag[iatoms] == atom2))) {
data.dihedral_type[data.idihedrals] = type;
data.dihedral_atom1[data.idihedrals] = atom1;
data.dihedral_atom2[data.idihedrals] = atom2;
data.dihedral_atom3[data.idihedrals] = atom3;
data.dihedral_atom4[data.idihedrals] = atom4;
data.idihedrals++;
}
}
n = static_cast<int> (buf[m++]);
for (int k = 0; k < n; k++) {
type = static_cast<int> (buf[m++]);
atom1 = static_cast<int> (buf[m++]);
atom2 = static_cast<int> (buf[m++]);
atom3 = static_cast<int> (buf[m++]);
atom4 = static_cast<int> (buf[m++]);
if ((type != 0) && (data.newton_bond || (data.tag[iatoms] == atom2))) {
data.improper_type[data.iimpropers] = type;
data.improper_atom1[data.iimpropers] = atom1;
data.improper_atom2[data.iimpropers] = atom2;
data.improper_atom3[data.iimpropers] = atom3;
data.improper_atom4[data.iimpropers] = atom4;
data.iimpropers++;
}
}
return m;
}
int atom_line(double *buf, Data &data, int iatoms)
{
fprintf(stderr,"Support for atom style line is not fully implemented\n");
exit(1);
}
int atom_meso(double *buf, Data &data, int iatoms)
{
fprintf(stderr,"Support for atom style meso is not fully implemented\n");
exit(1);
}
int atom_molecular(double *buf, Data &data, int iatoms)
{
int type,atom1,atom2,atom3,atom4;
int m = 1;
data.x[iatoms] = buf[m++];
data.y[iatoms] = buf[m++];
data.z[iatoms] = buf[m++];
data.tag[iatoms] = static_cast<int> (buf[m++]);
data.type[iatoms] = static_cast<int> (buf[m++]);
data.mask[iatoms] = static_cast<int> (buf[m++]);
data.image[iatoms] = *((tagint *) &buf[m++]);
data.vx[iatoms] = buf[m++];
data.vy[iatoms] = buf[m++];
data.vz[iatoms] = buf[m++];
data.molecule[iatoms] = static_cast<int> (buf[m++]);
int n = static_cast<int> (buf[m++]);
for (int k = 0; k < n; k++) {
type = static_cast<int> (buf[m++]);
atom1 = static_cast<int> (buf[m++]);
if ((type != 0) && (data.newton_bond || (data.tag[iatoms] < atom1))) {
data.bond_type[data.ibonds] = type;
data.bond_atom1[data.ibonds] = data.tag[iatoms];
data.bond_atom2[data.ibonds] = atom1;
data.ibonds++;
}
}
n = static_cast<int> (buf[m++]);
for (int k = 0; k < n; k++) {
type = static_cast<int> (buf[m++]);
atom1 = static_cast<int> (buf[m++]);
atom2 = static_cast<int> (buf[m++]);
atom3 = static_cast<int> (buf[m++]);
if ((type != 0) && (data.newton_bond || (data.tag[iatoms] == atom2))) {
data.angle_type[data.iangles] = type;
data.angle_atom1[data.iangles] = atom1;
data.angle_atom2[data.iangles] = atom2;
data.angle_atom3[data.iangles] = atom3;
data.iangles++;
}
}
n = static_cast<int> (buf[m++]);
for (int k = 0; k < n; k++) {
type = static_cast<int> (buf[m++]);
atom1 = static_cast<int> (buf[m++]);
atom2 = static_cast<int> (buf[m++]);
atom3 = static_cast<int> (buf[m++]);
atom4 = static_cast<int> (buf[m++]);
if ((type != 0) && (data.newton_bond || (data.tag[iatoms] == atom2))) {
data.dihedral_type[data.idihedrals] = type;
data.dihedral_atom1[data.idihedrals] = atom1;
data.dihedral_atom2[data.idihedrals] = atom2;
data.dihedral_atom3[data.idihedrals] = atom3;
data.dihedral_atom4[data.idihedrals] = atom4;
data.idihedrals++;
}
}
n = static_cast<int> (buf[m++]);
for (int k = 0; k < n; k++) {
type = static_cast<int> (buf[m++]);
atom1 = static_cast<int> (buf[m++]);
atom2 = static_cast<int> (buf[m++]);
atom3 = static_cast<int> (buf[m++]);
atom4 = static_cast<int> (buf[m++]);
if ((type != 0) && (data.newton_bond || (data.tag[iatoms] == atom2))) {
data.improper_type[data.iimpropers] = type;
data.improper_atom1[data.iimpropers] = atom1;
data.improper_atom2[data.iimpropers] = atom2;
data.improper_atom3[data.iimpropers] = atom3;
data.improper_atom4[data.iimpropers] = atom4;
data.iimpropers++;
}
}
return m;
}
int atom_peri(double *buf, Data &data, int iatoms)
{
int m = 1;
data.x[iatoms] = buf[m++];
data.y[iatoms] = buf[m++];
data.z[iatoms] = buf[m++];
data.tag[iatoms] = static_cast<int> (buf[m++]);
data.type[iatoms] = static_cast<int> (buf[m++]);
data.mask[iatoms] = static_cast<int> (buf[m++]);
data.image[iatoms] = *((tagint *) &buf[m++]);
data.vx[iatoms] = buf[m++];
data.vy[iatoms] = buf[m++];
data.vz[iatoms] = buf[m++];
data.vfrac[iatoms] = buf[m++];
data.rmass[iatoms] = buf[m++];
data.s0[iatoms] = buf[m++];
data.x0x[iatoms] = buf[m++];
data.x0y[iatoms] = buf[m++];
data.x0z[iatoms] = buf[m++];
return m;
}
int atom_sphere(double *buf, Data &data, int iatoms)
{
int m = 1;
data.x[iatoms] = buf[m++];
data.y[iatoms] = buf[m++];
data.z[iatoms] = buf[m++];
data.tag[iatoms] = static_cast<int> (buf[m++]);
data.type[iatoms] = static_cast<int> (buf[m++]);
data.mask[iatoms] = static_cast<int> (buf[m++]);
data.image[iatoms] = *((tagint *) &buf[m++]);
data.vx[iatoms] = buf[m++];
data.vy[iatoms] = buf[m++];
data.vz[iatoms] = buf[m++];
data.radius[iatoms] = buf[m++];
data.rmass[iatoms] = buf[m++];
if (data.radius[iatoms] == 0.0) data.density[iatoms] = data.rmass[iatoms];
else
data.density[iatoms] = data.rmass[iatoms] /
(4.0*PI/3.0 *
data.radius[iatoms]*data.radius[iatoms]*data.radius[iatoms]);
data.omegax[iatoms] = buf[m++];
data.omegay[iatoms] = buf[m++];
data.omegaz[iatoms] = buf[m++];
return m;
}
int atom_tri(double *buf, Data &data, int iatoms)
{
fprintf(stderr,"Support for atom style tri is not fully implemented\n");
exit(1);
}
int atom_wavepacket(double *buf, Data &data, int iatoms)
{
fprintf(stderr,"Support for atom style wavepacket is not "
"fully implemented\n");
exit(1);
}
// ---------------------------------------------------------------------
// per-atom memory allocation routines
// one routine per atom style
// ---------------------------------------------------------------------
void allocate_angle(Data &data)
{
data.molecule = new int[data.natoms];
data.bond_type = new int[data.nbonds];
data.bond_atom1 = new int[data.nbonds];
data.bond_atom2 = new int[data.nbonds];
data.angle_type = new int[data.nangles];
data.angle_atom1 = new int[data.nangles];
data.angle_atom2 = new int[data.nangles];
data.angle_atom3 = new int[data.nangles];
}
void allocate_atomic(Data &data) {}
void allocate_bond(Data &data)
{
data.molecule = new int[data.natoms];
data.bond_type = new int[data.nbonds];
data.bond_atom1 = new int[data.nbonds];
data.bond_atom2 = new int[data.nbonds];
}
void allocate_charge(Data &data)
{
data.q = new double[data.natoms];
}
void allocate_dipole(Data &data)
{
data.q = new double[data.natoms];
data.mux = new double[data.natoms];
data.muy = new double[data.natoms];
data.muz = new double[data.natoms];
data.mul = new double[data.natoms];
}
void allocate_full(Data &data)
{
data.q = new double[data.natoms];
data.molecule = new int[data.natoms];
data.bond_type = new int[data.nbonds];
data.bond_atom1 = new int[data.nbonds];
data.bond_atom2 = new int[data.nbonds];
data.angle_type = new int[data.nangles];
data.angle_atom1 = new int[data.nangles];
data.angle_atom2 = new int[data.nangles];
data.angle_atom3 = new int[data.nangles];
data.dihedral_type = new int[data.ndihedrals];
data.dihedral_atom1 = new int[data.ndihedrals];
data.dihedral_atom2 = new int[data.ndihedrals];
data.dihedral_atom3 = new int[data.ndihedrals];
data.dihedral_atom4 = new int[data.ndihedrals];
data.improper_type = new int[data.nimpropers];
data.improper_atom1 = new int[data.nimpropers];
data.improper_atom2 = new int[data.nimpropers];
data.improper_atom3 = new int[data.nimpropers];
data.improper_atom4 = new int[data.nimpropers];
}
void allocate_ellipsoid(Data &data)
{
data.rmass = new double[data.natoms];
data.density = new double[data.natoms];
data.angmomx = new double[data.natoms];
data.angmomy = new double[data.natoms];
data.angmomz = new double[data.natoms];
data.ellipsoid = new int[data.natoms];
data.quatw = new double[data.natoms];
data.shapex = new double[data.natoms];
data.shapey = new double[data.natoms];
data.shapez = new double[data.natoms];
data.quati = new double[data.natoms];
data.quatj = new double[data.natoms];
data.quatk = new double[data.natoms];
}
void allocate_sphere(Data &data)
{
data.radius = new double[data.natoms];
data.rmass = new double[data.natoms];
data.density = new double[data.natoms];
data.omegax = new double[data.natoms];
data.omegay = new double[data.natoms];
data.omegaz = new double[data.natoms];
}
void allocate_molecular(Data &data)
{
data.molecule = new int[data.natoms];
data.bond_type = new int[data.nbonds];
data.bond_atom1 = new int[data.nbonds];
data.bond_atom2 = new int[data.nbonds];
data.angle_type = new int[data.nangles];
data.angle_atom1 = new int[data.nangles];
data.angle_atom2 = new int[data.nangles];
data.angle_atom3 = new int[data.nangles];
data.dihedral_type = new int[data.ndihedrals];
data.dihedral_atom1 = new int[data.ndihedrals];
data.dihedral_atom2 = new int[data.ndihedrals];
data.dihedral_atom3 = new int[data.ndihedrals];
data.dihedral_atom4 = new int[data.ndihedrals];
data.improper_type = new int[data.nimpropers];
data.improper_atom1 = new int[data.nimpropers];
data.improper_atom2 = new int[data.nimpropers];
data.improper_atom3 = new int[data.nimpropers];
data.improper_atom4 = new int[data.nimpropers];
}
void allocate_peri(Data &data)
{
data.vfrac = new double[data.natoms];
data.rmass = new double[data.natoms];
data.s0 = new double[data.natoms];
data.x0x = new double[data.natoms];
data.x0y = new double[data.natoms];
data.x0z = new double[data.natoms];
}
void allocate_line(Data &data)
{
fprintf(stderr,"support for atom style line is not fully implemented\n");
exit(1);
}
void allocate_meso(Data &data)
{
fprintf(stderr,"support for atom style meso is not fully implemented\n");
exit(1);
}
void allocate_tri(Data &data)
{
fprintf(stderr,"support for atom style tri is not fully implemented\n");
exit(1);
}
void allocate_wavepacket(Data &data)
{
fprintf(stderr,"support for atom style wavepacket is not fully implemented\n");
exit(1);
}
// ---------------------------------------------------------------------
// pair coeffs
// one section for each pair style
// flag = 1, read all coeff info and allocation arrays
// flag = 0, just read global settings (when called recursively by hybrid)
// ---------------------------------------------------------------------
void pair(FILE *fp, Data &data, char *style, int flag)
{
int i,j,m;
int itmp;
double rtmp;
if (strcmp(style,"none") == 0) {
} else if (strcmp(style,"adp") == 0) {
} else if (strcmp(style,"airebo") == 0) {
} else if (strcmp(style,"born/coul/long") == 0) {
double cut_lj_global = read_double(fp);
double cut_coul = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
int tail_flag = read_int(fp);
if (!flag) return;
data.pair_born_A = new double[data.ntypes+1];
data.pair_born_rho = new double[data.ntypes+1];
data.pair_born_sigma = new double[data.ntypes+1];
data.pair_born_C = new double[data.ntypes+1];
data.pair_born_D = new double[data.ntypes+1];
for (i = 1; i <= data.ntypes; i++)
for (j = i; j <= data.ntypes; j++) {
itmp = read_int(fp);
if (i == j && itmp == 0) {
printf("ERROR: Pair coeff %d,%d is not in restart file\n",i,j);
exit(1);
}
if (itmp) {
if (i == j) {
data.pair_born_A[i] = read_double(fp);
data.pair_born_rho[i] = read_double(fp);
data.pair_born_sigma[i] = read_double(fp);
data.pair_born_C[i] = read_double(fp);
data.pair_born_D[i] = read_double(fp);
double cut_lj = read_double(fp);
} else {
double born_A = read_double(fp);
double born_rho = read_double(fp);
double born_sigma = read_double(fp);
double born_C = read_double(fp);
double born_D = read_double(fp);
double cut_lj = read_double(fp);
}
}
}
} else if (strcmp(style,"brownian") == 0) {
double mu = read_double(fp);
int flaglog = read_int(fp);
int flagfld = read_int(fp);
double cut_inner_global = read_double(fp);
double cut_global = read_double(fp);
double t_target = read_double(fp);
int seed = read_int(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
int flagHI = read_int(fp);
int flagVF = read_int(fp);
if (!flag) return;
for (i = 1; i <= data.ntypes; i++)
for (j = i; j <= data.ntypes; j++) {
itmp = read_int(fp);
if (i == j && itmp == 0) {
printf("ERROR: Pair coeff %d,%d is not in restart file\n",i,j);
exit(1);
}
if (itmp) {
if (i == j) {
double cut_inner = read_double(fp);
double cut = read_double(fp);
} else {
double cut_inner = read_double(fp);
double cut = read_double(fp);
}
}
}
} else if ((strcmp(style,"buck") == 0) ||
(strcmp(style,"buck/coul/cut") == 0) ||
(strcmp(style,"buck/coul/long") == 0) ||
(strcmp(style,"buck/long/coul/long") == 0)) {
if (strcmp(style,"buck") == 0) {
m = 0;
double cut_lj_global = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
int tail_flag = read_int(fp);
} else if (strcmp(style,"buck/coul/cut") == 0) {
m = 1;
double cut_lj_global = read_double(fp);
double cut_lj_coul = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
int tail_flag = read_int(fp);
} else if (strcmp(style,"buck/coul/long") == 0) {
m = 0;
double cut_lj_global = read_double(fp);
double cut_lj_coul = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
int tail_flag = read_int(fp);
} else if (strcmp(style,"buck/long/coul/long") == 0) {
m = 0;
double cut_buck_global = read_double(fp);
double cut_coul = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
int ncoultablebits = read_int(fp);
double tabinner = read_double(fp);
int ewald_order = read_int(fp);
}
if (!flag) return;
data.pair_buck_A = new double[data.ntypes+1];
data.pair_buck_rho = new double[data.ntypes+1];
data.pair_buck_C = new double[data.ntypes+1];
for (i = 1; i <= data.ntypes; i++)
for (j = i; j <= data.ntypes; j++) {
itmp = read_int(fp);
if (i == j && itmp == 0) {
printf("ERROR: Pair coeff %d,%d is not in restart file\n",i,j);
exit(1);
}
if (itmp) {
if (i == j) {
data.pair_buck_A[i] = read_double(fp);
data.pair_buck_rho[i] = read_double(fp);
data.pair_buck_C[i] = read_double(fp);
double cut_lj = read_double(fp);
if (m) double cut_coul = read_double(fp);
} else {
double buck_A = read_double(fp);
double buck_rho = read_double(fp);
double buck_C = read_double(fp);
double cut_lj = read_double(fp);
if (m) double cut_coul = read_double(fp);
}
}
}
} else if (strcmp(style,"colloid") == 0) {
double cut_global = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
if (!flag) return;
data.pair_colloid_A12 = new double[data.ntypes+1];
data.pair_colloid_sigma = new double[data.ntypes+1];
data.pair_colloid_d1 = new double[data.ntypes+1];
data.pair_colloid_d2 = new double[data.ntypes+1];
for (i = 1; i <= data.ntypes; i++)
for (j = i; j <= data.ntypes; j++) {
itmp = read_int(fp);
if (i == j && itmp == 0) {
printf("ERROR: Pair coeff %d,%d is not in restart file\n",i,j);
exit(1);
}
if (itmp) {
if (i == j) {
data.pair_colloid_A12[i] = read_double(fp);
data.pair_colloid_sigma[i] = read_double(fp);
data.pair_colloid_d1[i] = read_double(fp);
data.pair_colloid_d2[i] = read_double(fp);
double cut_lj = read_double(fp);
} else {
double colloid_A12 = read_double(fp);
double colloid_sigma = read_double(fp);
double colloid_d1 = read_double(fp);
double colloid_d2 = read_double(fp);
double cut_lj = read_double(fp);
}
}
}
} else if (strcmp(style,"comb") == 0) {
} else if (strcmp(style,"coul/diel") == 0) {
m = 1;
double cut_coul = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
if (!flag) return;
for (i = 1; i <= data.ntypes; i++)
for (j = i; j <= data.ntypes; j++) {
itmp = read_int(fp);
if (i == j && itmp == 0) {
printf("ERROR: Pair coeff %d,%d is not in restart file\n",i,j);
exit(1);
}
if (itmp) {
if (i == j) {
double diel_rme = read_double(fp);
double diel_sigmae = read_double(fp);
double cut_coul = read_double(fp);
} else {
double diel_rme = read_double(fp);
double diel_sigmae = read_double(fp);
double cut_coul = read_double(fp);
}
}
}
} else if ((strcmp(style,"coul/cut") == 0) ||
(strcmp(style,"coul/debye") == 0)) {
if (strcmp(style,"coul/cut") == 0) {
double cut_coul = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
} else if (strcmp(style,"coul/debye") == 0) {
m = 1;
double cut_coul = read_double(fp);
double kappa = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
}
if (!flag) return;
for (i = 1; i <= data.ntypes; i++)
for (j = i; j <= data.ntypes; j++) {
itmp = read_int(fp);
if (i == j && itmp == 0) {
printf("ERROR: Pair coeff %d,%d is not in restart file\n",i,j);
exit(1);
}
if (itmp) {
if (i == j) {
double cut_coul = read_double(fp);
} else {
double cut_coul = read_double(fp);
}
}
}
} else if (strcmp(style,"coul/long") == 0) {
double cut_coul = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
int ncoultablebits = read_int(fp);
double tabinner = read_double(fp);
if (!flag) return;
} else if (strcmp(style,"dipole/cut") == 0) {
double cut_lj_global = read_double(fp);
double cut_coul_global = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
if (!flag) return;
data.pair_dipole_epsilon = new double[data.ntypes+1];
data.pair_dipole_sigma = new double[data.ntypes+1];
for (i = 1; i <= data.ntypes; i++)
for (j = i; j <= data.ntypes; j++) {
itmp = read_int(fp);
if (i == j && itmp == 0) {
printf("ERROR: Pair coeff %d,%d is not in restart file\n",i,j);
exit(1);
}
if (itmp) {
if (i == j) {
data.pair_dipole_epsilon[i] = read_double(fp);
data.pair_dipole_sigma[i] = read_double(fp);
double cut_lj = read_double(fp);
double cut_coul = read_double(fp);
} else {
double dipole_epsilon = read_double(fp);
double dipole_sigma = read_double(fp);
double cut_lj = read_double(fp);
double cut_coul = read_double(fp);
}
}
}
} else if (strcmp(style,"dipole/sf") == 0) {
double cut_lj_global = read_double(fp);
double cut_coul_global = read_double(fp);
int mix_flag = read_int(fp);
if (!flag) return;
data.pair_dipole_epsilon = new double[data.ntypes+1];
data.pair_dipole_sigma = new double[data.ntypes+1];
for (i = 1; i <= data.ntypes; i++)
for (j = i; j <= data.ntypes; j++) {
itmp = read_int(fp);
if (i == j && itmp == 0) {
printf("ERROR: Pair coeff %d,%d is not in restart file\n",i,j);
exit(1);
}
if (itmp) {
if (i == j) {
data.pair_dipole_epsilon[i] = read_double(fp);
data.pair_dipole_sigma[i] = read_double(fp);
double cut_lj = read_double(fp);
double cut_coul = read_double(fp);
} else {
double dipole_epsilon = read_double(fp);
double dipole_sigma = read_double(fp);
double cut_lj = read_double(fp);
double cut_coul = read_double(fp);
}
}
}
} else if (strcmp(style,"dpd") == 0) {
double temperature = read_double(fp);
double cut_global = read_double(fp);
int seed = read_int(fp);
int mix_flag = read_int(fp);
if (!flag) return;
data.pair_dpd_a0 = new double[data.ntypes+1];
data.pair_dpd_gamma = new double[data.ntypes+1];
for (i = 1; i <= data.ntypes; i++)
for (j = i; j <= data.ntypes; j++) {
itmp = read_int(fp);
if (i == j && itmp == 0) {
printf("ERROR: Pair coeff %d,%d is not in restart file\n",i,j);
exit(1);
}
if (itmp) {
if (i == j) {
data.pair_dpd_a0[i] = read_double(fp);
data.pair_dpd_gamma[i] = read_double(fp);
double cut = read_double(fp);
} else {
double dpd_a0 = read_double(fp);
double dpd_gamma = read_double(fp);
double cut = read_double(fp);
}
}
}
} else if (strcmp(style,"dpd/tstat") == 0) {
double tstart = read_double(fp);
double tstop = read_double(fp);
double cut_global = read_double(fp);
int seed = read_int(fp);
int mix_flag = read_int(fp);
if (!flag) return;
data.pair_dpd_a0 = new double[data.ntypes+1];
data.pair_dpd_gamma = new double[data.ntypes+1];
for (i = 1; i <= data.ntypes; i++)
for (j = i; j <= data.ntypes; j++) {
itmp = read_int(fp);
if (i == j && itmp == 0) {
printf("ERROR: Pair coeff %d,%d is not in restart file\n",i,j);
exit(1);
}
if (itmp) {
if (i == j) {
data.pair_dpd_a0[i] = read_double(fp);
data.pair_dpd_gamma[i] = read_double(fp);
double cut = read_double(fp);
} else {
double dpd_a0 = read_double(fp);
double dpd_gamma = read_double(fp);
double cut = read_double(fp);
}
}
}
} else if (strcmp(style,"eam") == 0) {
} else if (strcmp(style,"eam/alloy") == 0) {
} else if (strcmp(style,"eam/fs") == 0) {
} else if (strcmp(style,"eim") == 0) {
} else if (strcmp(style,"eff/cut") == 0) {
double cut_coul = read_double(fp);
int limit_size_flag = read_int(fp);
int flexible_pressure_flag = read_int(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
if (!flag) return;
for (i = 1; i <= data.ntypes; i++)
for (j = i; j <= data.ntypes; j++) {
itmp = read_int(fp);
if (i == j && itmp == 0) {
printf("ERROR: Pair coeff %d,%d is not in restart file\n",i,j);
exit(1);
}
if (itmp) {
if (i == j) {
double cut = read_double(fp);
} else {
double cut = read_double(fp);
}
}
}
} else if (strcmp(style,"gayberne") == 0) {
double gamma = read_double(fp);
double upsilon = read_double(fp);
double mu = read_double(fp);
double cut_global = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
if (!flag) return;
data.pair_gb_epsilon = new double[data.ntypes+1];
data.pair_gb_sigma = new double[data.ntypes+1];
data.pair_gb_epsa = new double[data.ntypes+1];
data.pair_gb_epsb = new double[data.ntypes+1];
data.pair_gb_epsc = new double[data.ntypes+1];
for (i = 1; i <= data.ntypes; i++) {
itmp = read_int(fp);
if (itmp) {
data.pair_gb_epsa[i] = read_double(fp);
data.pair_gb_epsb[i] = read_double(fp);
data.pair_gb_epsc[i] = read_double(fp);
data.pair_gb_epsa[i] = pow(data.pair_gb_epsa[i],-mu);
data.pair_gb_epsb[i] = pow(data.pair_gb_epsb[i],-mu);
data.pair_gb_epsc[i] = pow(data.pair_gb_epsc[i],-mu);
}
for (j = i; j <= data.ntypes; j++) {
itmp = read_int(fp);
if (i == j && itmp == 0) {
printf("ERROR: Pair coeff %d,%d is not in restart file\n",i,j);
exit(1);
}
if (itmp) {
if (i == j) {
data.pair_gb_epsilon[i] = read_double(fp);
data.pair_gb_sigma[i] = read_double(fp);
double cut = read_double(fp);
} else {
double gb_epsilon = read_double(fp);
double gb_sigma = read_double(fp);
double cut = read_double(fp);
}
}
}
}
} else if (strcmp(style,"gauss") == 0) {
double cut_lj_global = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
if (!flag) return;
data.pair_gauss_hgauss = new double[data.ntypes+1];
data.pair_gauss_rmh = new double[data.ntypes+1];
for (i = 1; i <= data.ntypes; i++)
for (j = i; j <= data.ntypes; j++) {
itmp = read_int(fp);
if (i == j && itmp == 0) {
printf("ERROR: Pair coeff %d,%d is not in restart file\n",i,j);
exit(1);
}
if (itmp) {
if (i == j) {
data.pair_gauss_hgauss[i] = read_double(fp);
data.pair_gauss_rmh[i] = read_double(fp);
double cut_lj = read_double(fp);
} else {
double dipole_hgauss = read_double(fp);
double dipole_rmh = read_double(fp);
double cut_lj = read_double(fp);
}
}
}
} else if (strcmp(style,"gauss/cut") == 0) {
double cut_lj_global = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
if (!flag) return;
data.pair_gauss_hgauss = new double[data.ntypes+1];
data.pair_gauss_rmh = new double[data.ntypes+1];
data.pair_gauss_sigmah = new double[data.ntypes+1];
for (i = 1; i <= data.ntypes; i++)
for (j = i; j <= data.ntypes; j++) {
itmp = read_int(fp);
if (i == j && itmp == 0) {
printf("ERROR: Pair coeff %d,%d is not in restart file\n",i,j);
exit(1);
}
if (itmp) {
if (i == j) {
data.pair_gauss_hgauss[i] = read_double(fp);
data.pair_gauss_rmh[i] = read_double(fp);
data.pair_gauss_sigmah[i] = read_double(fp);
double cut_lj = read_double(fp);
} else {
double dipole_hgauss = read_double(fp);
double dipole_rmh = read_double(fp);
double dipole_sigmah = read_double(fp);
double cut_lj = read_double(fp);
}
}
}
} else if ((strcmp(style,"gran/hooke") == 0) ||
(strcmp(style,"gran/hooke/history") == 0) ||
(strcmp(style,"gran/hertz/history") == 0)) {
double kn = read_double(fp);
double kt = read_double(fp);
double gamman = read_double(fp);
double gammat = read_double(fp);
double xmu = read_double(fp);
int dampflag = read_int(fp);
if (!flag) return;
for (i = 1; i <= data.ntypes; i++) {
for (j = i; j <= data.ntypes; j++) {
itmp = read_int(fp);
if (i == j && itmp == 0) {
printf("ERROR: Pair coeff %d,%d is not in restart file\n",i,j);
exit(1);
}
}
}
} else if ((strcmp(style,"lj/charmm/coul/charmm") == 0) ||
(strcmp(style,"lj/charmm/coul/charmm/implicit") == 0) ||
(strcmp(style,"lj/charmm/coul/long/proxy") == 0) ||
(strcmp(style,"lj/charmm/coul/long") == 0)) {
if (strcmp(style,"lj/charmm/coul/charmm") == 0) {
double cut_lj_inner = read_double(fp);
double cut_lj = read_double(fp);
double cut_coul_inner = read_double(fp);
double cut_coul = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
} else if (strcmp(style,"lj/charmm/coul/charmm/implicit") == 0) {
double cut_lj_inner = read_double(fp);
double cut_lj = read_double(fp);
double cut_coul_inner = read_double(fp);
double cut_coul = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
} else if (strcmp(style,"lj/charmm/coul/long/proxy") == 0) {
double cut_lj_inner = read_double(fp);
double cut_lj = read_double(fp);
double cut_coul = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
int ncoultablebits = read_int(fp);
double tabinner = read_double(fp);
} else if (strcmp(style,"lj/charmm/coul/long") == 0) {
double cut_lj_inner = read_double(fp);
double cut_lj = read_double(fp);
double cut_coul = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
int ncoultablebits = read_int(fp);
double tabinner = read_double(fp);
}
if (!flag) return;
data.pair_charmm_epsilon = new double[data.ntypes+1];
data.pair_charmm_sigma = new double[data.ntypes+1];
data.pair_charmm_eps14 = new double[data.ntypes+1];
data.pair_charmm_sigma14 = new double[data.ntypes+1];
for (i = 1; i <= data.ntypes; i++)
for (j = i; j <= data.ntypes; j++) {
itmp = read_int(fp);
if (i == j && itmp == 0) {
printf("ERROR: Pair coeff %d,%d is not in restart file\n",i,j);
exit(1);
}
if (itmp) {
if (i == j) {
data.pair_charmm_epsilon[i] = read_double(fp);
data.pair_charmm_sigma[i] = read_double(fp);
data.pair_charmm_eps14[i] = read_double(fp);
data.pair_charmm_sigma14[i] = read_double(fp);
} else {
double charmm_epsilon = read_double(fp);
double charmm_sigma = read_double(fp);
double charmm_eps14 = read_double(fp);
double charmm_sigma14 = read_double(fp);
}
}
}
} else if ((strcmp(style,"lj/class2") == 0) ||
(strcmp(style,"lj/class2/coul/cut") == 0) ||
(strcmp(style,"lj/class2/coul/long/proxy") == 0) ||
(strcmp(style,"lj/class2/coul/long") == 0)) {
if (strcmp(style,"lj/class2") == 0) {
m = 0;
double cut_lj_global = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
int tail_flag = read_int(fp);
} else if (strcmp(style,"lj/class2/coul/cut") == 0) {
m = 1;
double cut_lj_global = read_double(fp);
double cut_lj_coul = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
int tail_flag = read_int(fp);
} else if (strcmp(style,"lj/class2/coul/long/proxy") == 0) {
m = 0;
double cut_lj_global = read_double(fp);
double cut_lj_coul = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
int tail_flag = read_int(fp);
} else if (strcmp(style,"lj/class2/coul/long") == 0) {
m = 0;
double cut_lj_global = read_double(fp);
double cut_lj_coul = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
int tail_flag = read_int(fp);
}
if (!flag) return;
data.pair_class2_epsilon = new double[data.ntypes+1];
data.pair_class2_sigma = new double[data.ntypes+1];
for (i = 1; i <= data.ntypes; i++)
for (j = i; j <= data.ntypes; j++) {
itmp = read_int(fp);
if (i == j && itmp == 0) {
printf("ERROR: Pair coeff %d,%d is not in restart file\n",i,j);
exit(1);
}
if (itmp) {
if (i == j) {
data.pair_class2_epsilon[i] = read_double(fp);
data.pair_class2_sigma[i] = read_double(fp);
double cut_lj = read_double(fp);
if (m) double cut_coul = read_double(fp);
} else {
double class2_epsilon = read_double(fp);
double class2_sigma = read_double(fp);
double cut_lj = read_double(fp);
if (m) double cut_coul = read_double(fp);
}
}
}
} else if ((strcmp(style,"lj/cut") == 0) ||
(strcmp(style,"lj96/cut") == 0) ||
(strcmp(style,"lj/cut/coul/cut") == 0) ||
(strcmp(style,"lj/cut/coul/debye") == 0) ||
(strcmp(style,"lj/cut/coul/long") == 0) ||
(strcmp(style,"lj/cut/coul/long/proxy") == 0) ||
(strcmp(style,"lj/cut/tip4p/cut") == 0) ||
(strcmp(style,"lj/cut/tip4p/long") == 0) ||
(strcmp(style,"lj/long/coul/long") == 0)) {
if (strcmp(style,"lj/cut") == 0) {
m = 0;
double cut_lj_global = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
int tail_flag = read_int(fp);
} else if (strcmp(style,"lj96/cut") == 0) {
m = 0;
double cut_lj_global = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
int tail_flag = read_int(fp);
} else if (strcmp(style,"lj/cut/coul/cut") == 0) {
m = 1;
double cut_lj_global = read_double(fp);
double cut_lj_coul = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
int tail_flag = read_int(fp);
} else if (strcmp(style,"lj/cut/coul/debye") == 0) {
m = 1;
double cut_lj_global = read_double(fp);
double cut_lj_coul = read_double(fp);
double kappa = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
int tail_flag = read_int(fp);
} else if (strcmp(style,"lj/cut/coul/long") == 0) {
m = 0;
double cut_lj_global = read_double(fp);
double cut_lj_coul = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
int tail_flag = read_int(fp);
int ncoultablebits = read_int(fp);
double tabinner = read_double(fp);
} else if (strcmp(style,"lj/cut/coul/long/proxy") == 0) {
m = 0;
double cut_lj_global = read_double(fp);
double cut_lj_coul = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
int tail_flag = read_int(fp);
int ncoultablebits = read_int(fp);
double tabinner = read_double(fp);
} else if (strcmp(style,"lj/cut/tip4p/cut") == 0) {
m = 0;
int typeO = read_int(fp);
int typeH = read_int(fp);
int typeB = read_int(fp);
int typeA = read_int(fp);
double qdist = read_double(fp);
double cut_lj_global = read_double(fp);
double cut_lj_coul = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
int tail_flag = read_int(fp);
} else if (strcmp(style,"lj/cut/tip4p/long") == 0) {
m = 0;
int typeO = read_int(fp);
int typeH = read_int(fp);
int typeB = read_int(fp);
int typeA = read_int(fp);
double qdist = read_double(fp);
double cut_lj_global = read_double(fp);
double cut_lj_coul = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
int tail_flag = read_int(fp);
int ncoultablebits = read_int(fp);
double tabinner = read_double(fp);
} else if (strcmp(style,"lj/long/coul/long") == 0) {
m = 0;
double cut_lj_global = read_double(fp);
double cut_coul = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
int ncoultablebits = read_int(fp);
double tabinner = read_double(fp);
int ewald_order = read_int(fp);
}
if (!flag) return;
data.pair_lj_epsilon = new double[data.ntypes+1];
data.pair_lj_sigma = new double[data.ntypes+1];
for (i = 1; i <= data.ntypes; i++)
for (j = i; j <= data.ntypes; j++) {
itmp = read_int(fp);
if (i == j && itmp == 0) {
printf("ERROR: Pair coeff %d,%d is not in restart file\n",i,j);
exit(1);
}
if (itmp) {
if (i == j) {
data.pair_lj_epsilon[i] = read_double(fp);
data.pair_lj_sigma[i] = read_double(fp);
double cut_lj = read_double(fp);
if (m) double cut_coul = read_double(fp);
} else {
double lj_epsilon = read_double(fp);
double lj_sigma = read_double(fp);
double cut_lj = read_double(fp);
if (m) double cut_coul = read_double(fp);
}
}
}
} else if (strcmp(style,"lj/expand") == 0) {
double cut_global = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
int tail_flag = read_int(fp);
if (!flag) return;
data.pair_ljexpand_epsilon = new double[data.ntypes+1];
data.pair_ljexpand_sigma = new double[data.ntypes+1];
data.pair_ljexpand_shift = new double[data.ntypes+1];
for (i = 1; i <= data.ntypes; i++)
for (j = i; j <= data.ntypes; j++) {
itmp = read_int(fp);
if (i == j && itmp == 0) {
printf("ERROR: Pair coeff %d,%d is not in restart file\n",i,j);
exit(1);
}
if (itmp) {
if (i == j) {
data.pair_ljexpand_epsilon[i] = read_double(fp);
data.pair_ljexpand_sigma[i] = read_double(fp);
data.pair_ljexpand_shift[i] = read_double(fp);
double cut_lj = read_double(fp);
} else {
double ljexpand_epsilon = read_double(fp);
double ljexpand_sigma = read_double(fp);
double ljexpand_shift = read_double(fp);
double cut_lj = read_double(fp);
}
}
}
} else if ((strcmp(style,"lj/gromacs") == 0) ||
(strcmp(style,"lj/gromacs/coul/gromacs") == 0)) {
if (strcmp(style,"lj/gromacs") == 0) {
m = 1;
double cut_inner_global = read_double(fp);
double cut_global = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
} else if (strcmp(style,"lj/gromacs/coul/gromacs") == 0) {
m = 0;
double cut_lj_inner_global = read_double(fp);
double cut_lj = read_double(fp);
double cut_coul_inner_global = read_double(fp);
double cut_coul = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
}
if (!flag) return;
data.pair_ljgromacs_epsilon = new double[data.ntypes+1];
data.pair_ljgromacs_sigma = new double[data.ntypes+1];
for (i = 1; i <= data.ntypes; i++)
for (j = i; j <= data.ntypes; j++) {
itmp = read_int(fp);
if (i == j && itmp == 0) {
printf("ERROR: Pair coeff %d,%d is not in restart file\n",i,j);
exit(1);
}
if (itmp) {
if (i == j) {
data.pair_ljgromacs_epsilon[i] = read_double(fp);
data.pair_ljgromacs_sigma[i] = read_double(fp);
if (m) {
double cut_inner = read_double(fp);
double cut = read_double(fp);
}
} else {
double ljgromacs_epsilon = read_double(fp);
double ljgromacs_sigma = read_double(fp);
if (m) {
double cut_inner = read_double(fp);
double cut = read_double(fp);
}
}
}
}
} else if (strcmp(style,"lj/smooth") == 0) {
double cut_inner_global = read_double(fp);
double cut_global = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
if (!flag) return;
data.pair_ljsmooth_epsilon = new double[data.ntypes+1];
data.pair_ljsmooth_sigma = new double[data.ntypes+1];
for (i = 1; i <= data.ntypes; i++)
for (j = i; j <= data.ntypes; j++) {
itmp = read_int(fp);
if (i == j && itmp == 0) {
printf("ERROR: Pair coeff %d,%d is not in restart file\n",i,j);
exit(1);
}
if (itmp) {
if (i == j) {
data.pair_ljsmooth_epsilon[i] = read_double(fp);
data.pair_ljsmooth_sigma[i] = read_double(fp);
double cut_inner = read_double(fp);
double cut = read_double(fp);
} else {
double ljsmooth_epsilon = read_double(fp);
double ljsmooth_sigma = read_double(fp);
double cut_inner = read_double(fp);
double cut = read_double(fp);
}
}
}
} else if ((strcmp(style,"lubricate") == 0) ||
(strcmp(style,"lubricateU") == 0)) {
double mu = read_double(fp);
int flaglog = read_int(fp);
int flagfld = read_int(fp);
double cut_inner_global = read_double(fp);
double cut_global = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
int flagHI = read_int(fp);
int flagVF = read_int(fp);
if (!flag) return;
for (i = 1; i <= data.ntypes; i++)
for (j = i; j <= data.ntypes; j++) {
itmp = read_int(fp);
if (i == j && itmp == 0) {
printf("ERROR: Pair coeff %d,%d is not in restart file\n",i,j);
exit(1);
}
if (itmp) {
if (i == j) {
double cut_inner = read_double(fp);
double cut = read_double(fp);
} else {
double cut_inner = read_double(fp);
double cut = read_double(fp);
}
}
}
} else if ((strcmp(style,"meam") == 0) ||
(strcmp(style,"meam/spline") == 0)) {
} else if (strcmp(style,"morse") == 0) {
double cut_global = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
if (!flag) return;
data.pair_morse_d0 = new double[data.ntypes+1];
data.pair_morse_alpha = new double[data.ntypes+1];
data.pair_morse_r0 = new double[data.ntypes+1];
for (i = 1; i <= data.ntypes; i++)
for (j = i; j <= data.ntypes; j++) {
itmp = read_int(fp);
if (i == j && itmp == 0) {
printf("ERROR: Pair coeff %d,%d is not in restart file\n",i,j);
exit(1);
}
if (itmp) {
if (i == j) {
data.pair_morse_d0[i] = read_double(fp);
data.pair_morse_alpha[i] = read_double(fp);
data.pair_morse_r0[i] = read_double(fp);
double cut = read_double(fp);
} else {
double morse_d0 = read_double(fp);
double morse_alpha = read_double(fp);
double morse_r0 = read_double(fp);
double cut = read_double(fp);
}
}
}
} else if (strcmp(style,"reax") == 0) {
} else if (strcmp(style,"reax/c") == 0) {
} else if (strcmp(style,"soft") == 0) {
double cut_global = read_double(fp);
int mix_flag = read_int(fp);
if (!flag) return;
data.pair_soft_A = new double[data.ntypes+1];
for (i = 1; i <= data.ntypes; i++)
for (j = i; j <= data.ntypes; j++) {
itmp = read_int(fp);
if (i == j && itmp == 0) {
printf("ERROR: Pair coeff %d,%d is not in restart file\n",i,j);
exit(1);
}
if (itmp) {
if (i == j) {
data.pair_soft_A[i] = read_double(fp);
double cut = read_double(fp);
} else {
double soft_A = read_double(fp);
double cut = read_double(fp);
}
}
}
} else if (strcmp(style,"sw") == 0) {
} else if (strcmp(style,"table") == 0) {
int tabstyle = read_int(fp);
int n = read_int(fp);
} else if (strcmp(style,"tersoff") == 0) {
} else if (strcmp(style,"tersoff/table") == 0) {
} else if (strcmp(style,"tersoff/zbl") == 0) {
} else if ((strcmp(style,"yukawa") == 0) ||
(strcmp(style,"yukawa/colloid") == 0)) {
double kappa = read_double(fp);
double cut_global = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
if (!flag) return;
data.pair_yukawa_A = new double[data.ntypes+1];
for (i = 1; i <= data.ntypes; i++)
for (j = i; j <= data.ntypes; j++) {
itmp = read_int(fp);
if (i == j && itmp == 0) {
printf("ERROR: Pair coeff %d,%d is not in restart file\n",i,j);
exit(1);
}
if (itmp) {
if (i == j) {
data.pair_yukawa_A[i] = read_double(fp);
double cut = read_double(fp);
} else {
double yukawa_A = read_double(fp);
double cut = read_double(fp);
}
}
}
} else if ((strcmp(style,"cg/cmm") == 0) ||
(strcmp(style,"cg/cmm/coul/long") == 0) ||
(strcmp(style,"lj/sdk") == 0) ||
(strcmp(style,"lj/sdk/coul/long") == 0)) {
m = 0;
data.cut_lj_global = read_double(fp);
if ((strcmp(style,"cg/cmm/coul/long") == 0) ||
(strcmp(style,"lj/sdk/coul/long") == 0)) {
data.cut_coul_global = read_double(fp);
}
data.offset_flag = read_int(fp);
data.mix_flag = read_int(fp);
data.tail_flag = read_int(fp);
if ((strcmp(style,"cg/cmm/coul/long") == 0) ||
(strcmp(style,"lj/sdk/coul/long") == 0)) {
data.ncoultablebits = read_int(fp);
data.tabinner = read_double(fp);
}
if (!flag) return;
const int numtyp=data.ntypes+1;
data.pair_cg_cmm_type = new int*[numtyp];
data.pair_setflag = new int*[numtyp];
data.pair_cg_epsilon = new double*[numtyp];
data.pair_cg_sigma = new double*[numtyp];
data.pair_cut_lj = new double*[numtyp];
data.pair_cut_coul = NULL;
m=0;
for (i = 1; i <= data.ntypes; i++) {
data.pair_cg_cmm_type[i] = new int[numtyp];
data.pair_setflag[i] = new int[numtyp];
data.pair_cg_epsilon[i] = new double[numtyp];
data.pair_cg_sigma[i] = new double[numtyp];
data.pair_cut_lj[i] = new double[numtyp];
for (j = i; j <= data.ntypes; j++) {
itmp = read_int(fp);
data.pair_setflag[i][j] = itmp;
if (i == j && itmp == 0) {
printf("ERROR: Pair coeff %d,%d is not in restart file\n",i,j);
exit(1);
}
if (itmp) {
data.pair_cg_cmm_type[i][j] = read_int(fp);
data.pair_cg_epsilon[i][j] = read_double(fp);
data.pair_cg_sigma[i][j] = read_double(fp);
data.pair_cut_lj[i][j] = read_double(fp);
}
}
}
} else if ((strcmp(style,"cg/cmm/old") == 0) ||
(strcmp(style,"cg/cmm/coul/cut/old") == 0) ||
(strcmp(style,"cg/cmm/coul/long/old") == 0)) {
m = 0;
data.cut_lj_global = read_double(fp);
data.cut_coul_global = read_double(fp);
data.kappa = read_double(fp);
data.offset_flag = read_int(fp);
data.mix_flag = read_int(fp);
if (!flag) return;
const int numtyp=data.ntypes+1;
data.pair_cg_cmm_type = new int*[numtyp];
data.pair_setflag = new int*[numtyp];
data.pair_cg_epsilon = new double*[numtyp];
data.pair_cg_sigma = new double*[numtyp];
data.pair_cut_lj = new double*[numtyp];
if ((strcmp(style,"cg/cmm/coul/cut/old") == 0) ||
(strcmp(style,"cg/cmm/coul/long/old") == 0)) {
data.pair_cut_coul = new double*[numtyp];
m=1;
} else {
data.pair_cut_coul = NULL;
m=0;
}
for (i = 1; i <= data.ntypes; i++) {
data.pair_cg_cmm_type[i] = new int[numtyp];
data.pair_setflag[i] = new int[numtyp];
data.pair_cg_epsilon[i] = new double[numtyp];
data.pair_cg_sigma[i] = new double[numtyp];
data.pair_cut_lj[i] = new double[numtyp];
if ((strcmp(style,"cg/cmm/coul/cut/old") == 0) ||
(strcmp(style,"cg/cmm/coul/long/old") == 0)) {
data.pair_cut_coul[i] = new double[numtyp];
}
for (j = i; j <= data.ntypes; j++) {
itmp = read_int(fp);
data.pair_setflag[i][j] = itmp;
if (i == j && itmp == 0) {
printf("ERROR: Pair coeff %d,%d is not in restart file\n",i,j);
exit(1);
}
if (itmp) {
data.pair_cg_cmm_type[i][j] = read_int(fp);
data.pair_cg_epsilon[i][j] = read_double(fp);
data.pair_cg_sigma[i][j] = read_double(fp);
data.pair_cut_lj[i][j] = read_double(fp);
if (m) {
data.pair_cut_lj[i][j] = read_double(fp);
data.pair_cut_coul[i][j] = read_double(fp);
}
}
}
}
} else if ((strcmp(style,"hybrid") == 0) ||
(strcmp(style,"hybrid/overlay") == 0)) {
// for each substyle of hybrid,
// read its settings by calling pair() recursively with flag = 0
// so that coeff array allocation is skipped
int nstyles = read_int(fp);
for (int i = 0; i < nstyles; i++) {
char *substyle = read_char(fp);
strip_suffix(substyle);
pair(fp,data,substyle,0);
}
} else {
printf("ERROR: Unknown pair style %s\n",style);
exit(1);
}
}
// ---------------------------------------------------------------------
// bond coeffs
// one section for each bond style
// ---------------------------------------------------------------------
void bond(FILE *fp, Data &data)
{
if (strcmp(data.bond_style,"none") == 0) {
} else if (strcmp(data.bond_style,"class2") == 0) {
data.bond_class2_r0 = new double[data.nbondtypes+1];
data.bond_class2_k2 = new double[data.nbondtypes+1];
data.bond_class2_k3 = new double[data.nbondtypes+1];
data.bond_class2_k4 = new double[data.nbondtypes+1];
nread_double(&data.bond_class2_r0[1],data.nbondtypes,fp);
nread_double(&data.bond_class2_k2[1],data.nbondtypes,fp);
nread_double(&data.bond_class2_k3[1],data.nbondtypes,fp);
nread_double(&data.bond_class2_k4[1],data.nbondtypes,fp);
} else if (strcmp(data.bond_style,"fene") == 0) {
data.bond_fene_k = new double[data.nbondtypes+1];
data.bond_fene_r0 = new double[data.nbondtypes+1];
data.bond_fene_epsilon = new double[data.nbondtypes+1];
data.bond_fene_sigma = new double[data.nbondtypes+1];
nread_double(&data.bond_fene_k[1],data.nbondtypes,fp);
nread_double(&data.bond_fene_r0[1],data.nbondtypes,fp);
nread_double(&data.bond_fene_epsilon[1],data.nbondtypes,fp);
nread_double(&data.bond_fene_sigma[1],data.nbondtypes,fp);
} else if (strcmp(data.bond_style,"fene/expand") == 0) {
data.bond_feneexpand_k = new double[data.nbondtypes+1];
data.bond_feneexpand_r0 = new double[data.nbondtypes+1];
data.bond_feneexpand_epsilon = new double[data.nbondtypes+1];
data.bond_feneexpand_sigma = new double[data.nbondtypes+1];
data.bond_feneexpand_shift = new double[data.nbondtypes+1];
nread_double(&data.bond_feneexpand_k[1],data.nbondtypes,fp);
nread_double(&data.bond_feneexpand_r0[1],data.nbondtypes,fp);
nread_double(&data.bond_feneexpand_epsilon[1],data.nbondtypes,fp);
nread_double(&data.bond_feneexpand_sigma[1],data.nbondtypes,fp);
nread_double(&data.bond_feneexpand_shift[1],data.nbondtypes,fp);
} else if (strcmp(data.bond_style,"harmonic") == 0) {
data.bond_harmonic_k = new double[data.nbondtypes+1];
data.bond_harmonic_r0 = new double[data.nbondtypes+1];
nread_double(&data.bond_harmonic_k[1],data.nbondtypes,fp);
nread_double(&data.bond_harmonic_r0[1],data.nbondtypes,fp);
} else if (strcmp(data.bond_style,"harmonicshift") == 0) {
data.bond_harmonicshift_umin = new double[data.nbondtypes+1];
data.bond_harmonicshift_r0 = new double[data.nbondtypes+1];
data.bond_harmonicshift_rc = new double[data.nbondtypes+1];
nread_double(&data.bond_harmonicshift_umin[1],data.nbondtypes,fp);
nread_double(&data.bond_harmonicshift_r0[1],data.nbondtypes,fp);
nread_double(&data.bond_harmonicshift_rc[1],data.nbondtypes,fp);
} else if (strcmp(data.bond_style,"harmonicshiftcut") == 0) {
data.bond_harmonicshiftcut_umin = new double[data.nbondtypes+1];
data.bond_harmonicshiftcut_r0 = new double[data.nbondtypes+1];
data.bond_harmonicshiftcut_rc = new double[data.nbondtypes+1];
nread_double(&data.bond_harmonicshiftcut_umin[1],data.nbondtypes,fp);
nread_double(&data.bond_harmonicshiftcut_r0[1],data.nbondtypes,fp);
nread_double(&data.bond_harmonicshiftcut_rc[1],data.nbondtypes,fp);
} else if (strcmp(data.bond_style,"morse") == 0) {
data.bond_morse_d0 = new double[data.nbondtypes+1];
data.bond_morse_alpha = new double[data.nbondtypes+1];
data.bond_morse_r0 = new double[data.nbondtypes+1];
nread_double(&data.bond_morse_d0[1],data.nbondtypes,fp);
nread_double(&data.bond_morse_alpha[1],data.nbondtypes,fp);
nread_double(&data.bond_morse_r0[1],data.nbondtypes,fp);
} else if (strcmp(data.bond_style,"nonlinear") == 0) {
data.bond_nonlinear_epsilon = new double[data.nbondtypes+1];
data.bond_nonlinear_r0 = new double[data.nbondtypes+1];
data.bond_nonlinear_lamda = new double[data.nbondtypes+1];
nread_double(&data.bond_nonlinear_epsilon[1],data.nbondtypes,fp);
nread_double(&data.bond_nonlinear_r0[1],data.nbondtypes,fp);
nread_double(&data.bond_nonlinear_lamda[1],data.nbondtypes,fp);
} else if (strcmp(data.bond_style,"quartic") == 0) {
data.bond_quartic_k = new double[data.nbondtypes+1];
data.bond_quartic_b1 = new double[data.nbondtypes+1];
data.bond_quartic_b2 = new double[data.nbondtypes+1];
data.bond_quartic_rc = new double[data.nbondtypes+1];
data.bond_quartic_u0 = new double[data.nbondtypes+1];
nread_double(&data.bond_quartic_k[1],data.nbondtypes,fp);
nread_double(&data.bond_quartic_b1[1],data.nbondtypes,fp);
nread_double(&data.bond_quartic_b2[1],data.nbondtypes,fp);
nread_double(&data.bond_quartic_rc[1],data.nbondtypes,fp);
nread_double(&data.bond_quartic_u0[1],data.nbondtypes,fp);
} else if (strcmp(data.bond_style,"table") == 0) {
int tabstyle = read_int(fp);
int n = read_int(fp);
} else if (strcmp(data.bond_style,"hybrid") == 0) {
int nstyles = read_int(fp);
for (int i = 0; i < nstyles; i++)
char *substyle = read_char(fp);
} else {
printf("ERROR: Unknown bond style %s\n",data.bond_style);
exit(1);
}
}
// ---------------------------------------------------------------------
// angle coeffs
// one section for each angle style
// ---------------------------------------------------------------------
void angle(FILE *fp, Data &data)
{
if (strcmp(data.angle_style,"none") == 0) {
} else if ((strcmp(data.angle_style,"cg/cmm") == 0) ||
(strcmp(data.angle_style,"sdk") == 0)) {
data.angle_harmonic_k = new double[data.nangletypes+1];
data.angle_harmonic_theta0 = new double[data.nangletypes+1];
data.angle_cg_cmm_epsilon = new double[data.nangletypes+1];
nread_double(&data.angle_harmonic_k[1],data.nangletypes,fp);
nread_double(&data.angle_harmonic_theta0[1],data.nangletypes,fp);
nread_double(&data.angle_cg_cmm_epsilon[1],data.nangletypes,fp);
} else if (strcmp(data.angle_style,"cg/cmm/old") == 0) {
data.angle_harmonic_k = new double[data.nangletypes+1];
data.angle_harmonic_theta0 = new double[data.nangletypes+1];
data.angle_cg_cmm_epsilon = new double[data.nangletypes+1];
data.angle_cg_cmm_sigma = new double[data.nangletypes+1];
double *angle_cg_cmm_rcut = new double[data.nangletypes+1];
data.angle_cg_cmm_type = new int[data.nangletypes+1];
nread_double(&data.angle_harmonic_k[1],data.nangletypes,fp);
nread_double(&data.angle_harmonic_theta0[1],data.nangletypes,fp);
nread_double(&data.angle_cg_cmm_epsilon[1],data.nangletypes,fp);
nread_double(&data.angle_cg_cmm_sigma[1],data.nangletypes,fp);
nread_double(angle_cg_cmm_rcut,data.nangletypes,fp);
nread_int(&data.angle_cg_cmm_type[1],data.nangletypes,fp);
} else if (strcmp(data.angle_style,"charmm") == 0) {
data.angle_charmm_k = new double[data.nangletypes+1];
data.angle_charmm_theta0 = new double[data.nangletypes+1];
data.angle_charmm_k_ub = new double[data.nangletypes+1];
data.angle_charmm_r_ub = new double[data.nangletypes+1];
nread_double(&data.angle_charmm_k[1],data.nangletypes,fp);
nread_double(&data.angle_charmm_theta0[1],data.nangletypes,fp);
nread_double(&data.angle_charmm_k_ub[1],data.nangletypes,fp);
nread_double(&data.angle_charmm_r_ub[1],data.nangletypes,fp);
} else if (strcmp(data.angle_style,"class2") == 0) {
data.angle_class2_theta0 = new double[data.nangletypes+1];
data.angle_class2_k2 = new double[data.nangletypes+1];
data.angle_class2_k3 = new double[data.nangletypes+1];
data.angle_class2_k4 = new double[data.nangletypes+1];
data.angle_class2_bb_k = new double[data.nangletypes+1];
data.angle_class2_bb_r1 = new double[data.nangletypes+1];
data.angle_class2_bb_r2 = new double[data.nangletypes+1];
data.angle_class2_ba_k1 = new double[data.nangletypes+1];
data.angle_class2_ba_k2 = new double[data.nangletypes+1];
data.angle_class2_ba_r1 = new double[data.nangletypes+1];
data.angle_class2_ba_r2 = new double[data.nangletypes+1];
nread_double(&data.angle_class2_theta0[1],data.nangletypes,fp);
nread_double(&data.angle_class2_k2[1],data.nangletypes,fp);
nread_double(&data.angle_class2_k3[1],data.nangletypes,fp);
nread_double(&data.angle_class2_k4[1],data.nangletypes,fp);
nread_double(&data.angle_class2_bb_k[1],data.nangletypes,fp);
nread_double(&data.angle_class2_bb_r1[1],data.nangletypes,fp);
nread_double(&data.angle_class2_bb_r2[1],data.nangletypes,fp);
nread_double(&data.angle_class2_ba_k1[1],data.nangletypes,fp);
nread_double(&data.angle_class2_ba_k2[1],data.nangletypes,fp);
nread_double(&data.angle_class2_ba_r1[1],data.nangletypes,fp);
nread_double(&data.angle_class2_ba_r2[1],data.nangletypes,fp);
} else if (strcmp(data.angle_style,"cosineshift") == 0) {
data.angle_cosineshift_umin = new double[data.nangletypes+1];
nread_double(&data.angle_cosineshift_umin[1],data.nangletypes,fp);
data.angle_cosineshift_cost = new double[data.nangletypes+1];
nread_double(&data.angle_cosineshift_cost[1],data.nangletypes,fp);
data.angle_cosineshift_sint = new double[data.nangletypes+1];
nread_double(&data.angle_cosineshift_sint[1],data.nangletypes,fp);
data.angle_cosineshift_theta0 = new double[data.nangletypes+1];
nread_double(&data.angle_cosineshift_theta0[1],data.nangletypes,fp);
} else if (strcmp(data.angle_style,"cosineshiftexp") == 0) {
data.angle_cosineshiftexp_umin = new double[data.nangletypes+1];
nread_double(&data.angle_cosineshiftexp_umin[1],data.nangletypes,fp);
data.angle_cosineshiftexp_a = new double[data.nangletypes+1];
nread_double(&data.angle_cosineshiftexp_a[1],data.nangletypes,fp);
data.angle_cosineshiftexp_cost = new double[data.nangletypes+1];
nread_double(&data.angle_cosineshiftexp_cost[1],data.nangletypes,fp);
data.angle_cosineshiftexp_sint = new double[data.nangletypes+1];
nread_double(&data.angle_cosineshiftexp_sint[1],data.nangletypes,fp);
data.angle_cosineshiftexp_theta0 = new double[data.nangletypes+1];
nread_double(&data.angle_cosineshiftexp_theta0[1],data.nangletypes,fp);
} else if (strcmp(data.angle_style,"cosine") == 0) {
data.angle_cosine_k = new double[data.nangletypes+1];
nread_double(&data.angle_cosine_k[1],data.nangletypes,fp);
} else if ((strcmp(data.angle_style,"cosine/squared") == 0) ||
(strcmp(data.angle_style,"cosine/delta") == 0)) {
data.angle_cosine_squared_k = new double[data.nangletypes+1];
data.angle_cosine_squared_theta0 = new double[data.nangletypes+1];
nread_double(&data.angle_cosine_squared_k[1],data.nangletypes,fp);
nread_double(&data.angle_cosine_squared_theta0[1],data.nangletypes,fp);
} else if (strcmp(data.angle_style,"dipole") == 0) {
data.angle_harmonic_k = new double[data.nangletypes+1];
data.angle_harmonic_theta0 = new double[data.nangletypes+1];
nread_double(&data.angle_harmonic_k[1],data.nangletypes,fp);
nread_double(&data.angle_harmonic_theta0[1],data.nangletypes,fp);
} else if (strcmp(data.angle_style,"harmonic") == 0) {
data.angle_harmonic_k = new double[data.nangletypes+1];
data.angle_harmonic_theta0 = new double[data.nangletypes+1];
nread_double(&data.angle_harmonic_k[1],data.nangletypes,fp);
nread_double(&data.angle_harmonic_theta0[1],data.nangletypes,fp);
} else if (strcmp(data.angle_style,"table") == 0) {
int tabstyle = read_int(fp);
int n = read_int(fp);
} else if (strcmp(data.angle_style,"hybrid") == 0) {
int nstyles = read_int(fp);
for (int i = 0; i < nstyles; i++)
char *substyle = read_char(fp);
} else {
printf("ERROR: Unknown angle style %s\n",data.angle_style);
exit(1);
}
}
// ---------------------------------------------------------------------
// dihedral coeffs
// one section for each dihedral style
// ---------------------------------------------------------------------
void dihedral(FILE *fp, Data &data)
{
if (strcmp(data.dihedral_style,"none") == 0) {
} else if (strcmp(data.dihedral_style,"charmm") == 0) {
int dummy;
data.dihedral_charmm_k = new double[data.ndihedraltypes+1];
data.dihedral_charmm_multiplicity = new int[data.ndihedraltypes+1];
data.dihedral_charmm_sign = new int[data.ndihedraltypes+1];
data.dihedral_charmm_weight = new double[data.ndihedraltypes+1];
nread_double(&data.dihedral_charmm_k[1],data.ndihedraltypes,fp);
nread_int(&data.dihedral_charmm_multiplicity[1],data.ndihedraltypes,fp);
nread_int(&data.dihedral_charmm_sign[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_charmm_weight[1],data.ndihedraltypes,fp);
nread_int(&dummy,1,fp);
} else if (strcmp(data.dihedral_style,"class2") == 0) {
data.dihedral_class2_k1 = new double[data.ndihedraltypes+1];
data.dihedral_class2_k2 = new double[data.ndihedraltypes+1];
data.dihedral_class2_k3 = new double[data.ndihedraltypes+1];
data.dihedral_class2_phi1 = new double[data.ndihedraltypes+1];
data.dihedral_class2_phi2 = new double[data.ndihedraltypes+1];
data.dihedral_class2_phi3 = new double[data.ndihedraltypes+1];
data.dihedral_class2_mbt_f1 = new double[data.ndihedraltypes+1];
data.dihedral_class2_mbt_f2 = new double[data.ndihedraltypes+1];
data.dihedral_class2_mbt_f3 = new double[data.ndihedraltypes+1];
data.dihedral_class2_mbt_r0 = new double[data.ndihedraltypes+1];
data.dihedral_class2_ebt_f1_1 = new double[data.ndihedraltypes+1];
data.dihedral_class2_ebt_f2_1 = new double[data.ndihedraltypes+1];
data.dihedral_class2_ebt_f3_1 = new double[data.ndihedraltypes+1];
data.dihedral_class2_ebt_r0_1 = new double[data.ndihedraltypes+1];
data.dihedral_class2_ebt_f1_2 = new double[data.ndihedraltypes+1];
data.dihedral_class2_ebt_f2_2 = new double[data.ndihedraltypes+1];
data.dihedral_class2_ebt_f3_2 = new double[data.ndihedraltypes+1];
data.dihedral_class2_ebt_r0_2 = new double[data.ndihedraltypes+1];
data.dihedral_class2_at_f1_1 = new double[data.ndihedraltypes+1];
data.dihedral_class2_at_f2_1 = new double[data.ndihedraltypes+1];
data.dihedral_class2_at_f3_1 = new double[data.ndihedraltypes+1];
data.dihedral_class2_at_theta0_1 = new double[data.ndihedraltypes+1];
data.dihedral_class2_at_f1_2 = new double[data.ndihedraltypes+1];
data.dihedral_class2_at_f2_2 = new double[data.ndihedraltypes+1];
data.dihedral_class2_at_f3_2 = new double[data.ndihedraltypes+1];
data.dihedral_class2_at_theta0_2 = new double[data.ndihedraltypes+1];
data.dihedral_class2_aat_k = new double[data.ndihedraltypes+1];
data.dihedral_class2_aat_theta0_1 = new double[data.ndihedraltypes+1];
data.dihedral_class2_aat_theta0_2 = new double[data.ndihedraltypes+1];
data.dihedral_class2_bb13_k = new double[data.ndihedraltypes+1];
data.dihedral_class2_bb13_r10 = new double[data.ndihedraltypes+1];
data.dihedral_class2_bb13_r30 = new double[data.ndihedraltypes+1];
nread_double(&data.dihedral_class2_k1[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_class2_k2[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_class2_k3[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_class2_phi1[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_class2_phi2[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_class2_phi3[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_class2_mbt_f1[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_class2_mbt_f2[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_class2_mbt_f3[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_class2_mbt_r0[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_class2_ebt_f1_1[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_class2_ebt_f2_1[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_class2_ebt_f3_1[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_class2_ebt_r0_1[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_class2_ebt_f1_2[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_class2_ebt_f2_2[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_class2_ebt_f3_2[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_class2_ebt_r0_2[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_class2_at_f1_1[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_class2_at_f2_1[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_class2_at_f3_1[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_class2_at_theta0_1[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_class2_at_f1_2[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_class2_at_f2_2[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_class2_at_f3_2[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_class2_at_theta0_2[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_class2_aat_k[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_class2_aat_theta0_1[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_class2_aat_theta0_2[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_class2_bb13_k[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_class2_bb13_r10[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_class2_bb13_r30[1],data.ndihedraltypes,fp);
} else if (strcmp(data.dihedral_style,"harmonic") == 0) {
data.dihedral_harmonic_k = new double[data.ndihedraltypes+1];
data.dihedral_harmonic_multiplicity = new int[data.ndihedraltypes+1];
data.dihedral_harmonic_sign = new int[data.ndihedraltypes+1];
nread_double(&data.dihedral_harmonic_k[1],data.ndihedraltypes,fp);
nread_int(&data.dihedral_harmonic_multiplicity[1],data.ndihedraltypes,fp);
nread_int(&data.dihedral_harmonic_sign[1],data.ndihedraltypes,fp);
} else if (strcmp(data.dihedral_style,"helix") == 0) {
data.dihedral_helix_aphi = new double[data.ndihedraltypes+1];
data.dihedral_helix_bphi = new double[data.ndihedraltypes+1];
data.dihedral_helix_cphi = new double[data.ndihedraltypes+1];
nread_double(&data.dihedral_helix_aphi[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_helix_bphi[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_helix_cphi[1],data.ndihedraltypes,fp);
} else if (strcmp(data.dihedral_style,"multi/harmonic") == 0) {
data.dihedral_multi_a1 = new double[data.ndihedraltypes+1];
data.dihedral_multi_a2 = new double[data.ndihedraltypes+1];
data.dihedral_multi_a3 = new double[data.ndihedraltypes+1];
data.dihedral_multi_a4 = new double[data.ndihedraltypes+1];
data.dihedral_multi_a5 = new double[data.ndihedraltypes+1];
nread_double(&data.dihedral_multi_a1[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_multi_a2[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_multi_a3[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_multi_a4[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_multi_a5[1],data.ndihedraltypes,fp);
} else if (strcmp(data.dihedral_style,"opls") == 0) {
data.dihedral_opls_k1 = new double[data.ndihedraltypes+1];
data.dihedral_opls_k2 = new double[data.ndihedraltypes+1];
data.dihedral_opls_k3 = new double[data.ndihedraltypes+1];
data.dihedral_opls_k4 = new double[data.ndihedraltypes+1];
nread_double(&data.dihedral_opls_k1[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_opls_k2[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_opls_k3[1],data.ndihedraltypes,fp);
nread_double(&data.dihedral_opls_k4[1],data.ndihedraltypes,fp);
} else if (strcmp(data.dihedral_style,"cosineshiftexp") == 0) {
data.dihedral_cosineshiftexp_umin = new double[data.ndihedraltypes+1];
nread_double(&data.dihedral_cosineshiftexp_umin[1],data.ndihedraltypes,fp);
data.dihedral_cosineshiftexp_a = new double[data.ndihedraltypes+1];
nread_double(&data.dihedral_cosineshiftexp_a[1],data.ndihedraltypes,fp);
data.dihedral_cosineshiftexp_cost = new double[data.ndihedraltypes+1];
nread_double(&data.dihedral_cosineshiftexp_cost[1],data.ndihedraltypes,fp);
data.dihedral_cosineshiftexp_sint = new double[data.ndihedraltypes+1];
nread_double(&data.dihedral_cosineshiftexp_sint[1],data.ndihedraltypes,fp);
data.dihedral_cosineshiftexp_theta = new double[data.ndihedraltypes+1];
nread_double(&data.dihedral_cosineshiftexp_theta[1],data.ndihedraltypes,fp);
} else if (strcmp(data.dihedral_style,"table") == 0) {
int tabstyle = read_int(fp);
int n = read_int(fp);
} else if (strcmp(data.dihedral_style,"hybrid") == 0) {
int nstyles = read_int(fp);
for (int i = 0; i < nstyles; i++)
char *substyle = read_char(fp);
} else {
printf("ERROR: Unknown dihedral style %s\n",data.dihedral_style);
exit(1);
}
}
// ---------------------------------------------------------------------
// improper coeffs
// one section for each improper style
// ---------------------------------------------------------------------
void improper(FILE *fp, Data &data)
{
if (strcmp(data.improper_style,"none") == 0) {
} else if (strcmp(data.improper_style,"class2") == 0) {
data.improper_class2_k0 = new double[data.nimpropertypes+1];
data.improper_class2_chi0 = new double[data.nimpropertypes+1];
data.improper_class2_aa_k1 = new double[data.nimpropertypes+1];
data.improper_class2_aa_k2 = new double[data.nimpropertypes+1];
data.improper_class2_aa_k3 = new double[data.nimpropertypes+1];
data.improper_class2_aa_theta0_1 = new double[data.nimpropertypes+1];
data.improper_class2_aa_theta0_2 = new double[data.nimpropertypes+1];
data.improper_class2_aa_theta0_3 = new double[data.nimpropertypes+1];
nread_double(&data.improper_class2_k0[1],data.nimpropertypes,fp);
nread_double(&data.improper_class2_chi0[1],data.nimpropertypes,fp);
nread_double(&data.improper_class2_aa_k1[1],data.nimpropertypes,fp);
nread_double(&data.improper_class2_aa_k2[1],data.nimpropertypes,fp);
nread_double(&data.improper_class2_aa_k3[1],data.nimpropertypes,fp);
nread_double(&data.improper_class2_aa_theta0_1[1],data.nimpropertypes,fp);
nread_double(&data.improper_class2_aa_theta0_2[1],data.nimpropertypes,fp);
nread_double(&data.improper_class2_aa_theta0_3[1],data.nimpropertypes,fp);
} else if (strcmp(data.improper_style,"cvff") == 0) {
data.improper_cvff_k = new double[data.nimpropertypes+1];
data.improper_cvff_sign = new int[data.nimpropertypes+1];
data.improper_cvff_multiplicity = new int[data.nimpropertypes+1];
nread_double(&data.improper_cvff_k[1],data.nimpropertypes,fp);
nread_int(&data.improper_cvff_sign[1],data.nimpropertypes,fp);
nread_int(&data.improper_cvff_multiplicity[1],data.nimpropertypes,fp);
} else if (strcmp(data.improper_style,"harmonic") == 0) {
data.improper_harmonic_k = new double[data.nimpropertypes+1];
data.improper_harmonic_chi = new double[data.nimpropertypes+1];
nread_double(&data.improper_harmonic_k[1],data.nimpropertypes,fp);
nread_double(&data.improper_harmonic_chi[1],data.nimpropertypes,fp);
} else if (strcmp(data.improper_style,"hybrid") == 0) {
int nstyles = read_int(fp);
for (int i = 0; i < nstyles; i++)
char *substyle = read_char(fp);
} else {
printf("ERROR: Unknown improper style %s\n",data.improper_style);
exit(1);
}
}
// ---------------------------------------------------------------------
// initialize Data
// ---------------------------------------------------------------------
Data::Data()
{
nellipsoids = 0;
}
// ---------------------------------------------------------------------
// print out stats on problem
// ---------------------------------------------------------------------
void Data::stats()
{
char fstr[64];
printf(" Restart file version = %s\n",version);
printf(" Ntimestep = " BIGINT_FORMAT "\n",ntimestep);
printf(" Nprocs = %d\n",nprocs);
printf(" Natoms = " BIGINT_FORMAT "\n",natoms);
if (nellipsoids) printf(" Nellipsoids = " BIGINT_FORMAT "\n",nellipsoids);
if (ibonds) printf(" Nbonds = " BIGINT_FORMAT "\n",ibonds);
if (ibonds != nbonds)
printf(" Skipping " BIGINT_FORMAT " broken bonds\n",nbonds-ibonds);
if (iangles) printf(" Nangles = " BIGINT_FORMAT "\n",iangles);
if (iangles != nangles)
printf(" Skipping " BIGINT_FORMAT " broken angles\n",nangles-iangles);
if (idihedrals) printf(" Ndihedrals = " BIGINT_FORMAT "\n",idihedrals);
if (idihedrals != ndihedrals)
printf(" Skipping " BIGINT_FORMAT " broken dihedrals\n",
ndihedrals-idihedrals);
if (iimpropers) printf(" Nimpropers = " BIGINT_FORMAT "\n",iimpropers);
if (iimpropers != nimpropers)
printf(" Skipping " BIGINT_FORMAT " broken impropers\n",
nimpropers-iimpropers);
printf(" Unit style = %s\n",unit_style);
printf(" Atom style = %s\n",atom_style);
if (pair_style) printf(" Pair style = %s\n",pair_style);
if (bond_style) printf(" Bond style = %s\n",bond_style);
if (angle_style) printf(" Angle style = %s\n",angle_style);
if (dihedral_style) printf(" Dihedral style = %s\n",dihedral_style);
if (improper_style) printf(" Improper style = %s\n",improper_style);
printf(" Xlo xhi = %g %g\n",xlo,xhi);
printf(" Ylo yhi = %g %g\n",ylo,yhi);
printf(" Zlo zhi = %g %g\n",zlo,zhi);
if (triclinic) printf(" Xy xz yz = %g %g %g\n",xy,xz,yz);
printf(" Periodicity = %d %d %d\n",xperiodic,yperiodic,zperiodic);
printf(" Boundary = %d %d, %d %d, %d %d\n",boundary[0][0],boundary[0][1],
boundary[1][0],boundary[1][1],boundary[2][0],boundary[2][1]);
}
// ---------------------------------------------------------------------
// write the data file and input file
// ---------------------------------------------------------------------
void Data::write(FILE *fp, FILE *fp2, int write_coeffs, int write_vels)
{
fprintf(fp,"LAMMPS data file from restart file: timestep = "
BIGINT_FORMAT ", procs = %d\n\n",ntimestep,nprocs);
fprintf(fp,BIGINT_FORMAT " atoms\n",natoms);
if (nellipsoids) fprintf(fp,BIGINT_FORMAT " ellipsoids\n",nellipsoids);
if (ibonds) fprintf(fp,BIGINT_FORMAT " bonds\n",ibonds);
if (iangles) fprintf(fp,BIGINT_FORMAT " angles\n",iangles);
if (idihedrals) fprintf(fp,BIGINT_FORMAT " dihedrals\n",idihedrals);
if (iimpropers) fprintf(fp,BIGINT_FORMAT " impropers\n",iimpropers);
fprintf(fp,"\n");
fprintf(fp,"%d atom types\n",ntypes);
if (nbondtypes) fprintf(fp,"%d bond types\n",nbondtypes);
if (nangletypes) fprintf(fp,"%d angle types\n",nangletypes);
if (ndihedraltypes) fprintf(fp,"%d dihedral types\n",ndihedraltypes);
if (nimpropertypes) fprintf(fp,"%d improper types\n",nimpropertypes);
fprintf(fp,"\n");
fprintf(fp,"%-1.16e %-1.16e xlo xhi\n",xlo,xhi);
fprintf(fp,"%-1.16e %-1.16e ylo yhi\n",ylo,yhi);
fprintf(fp,"%-1.16e %-1.16e zlo zhi\n",zlo,zhi);
if (triclinic) fprintf(fp,"%-1.16e %-1.16e %-1.16e xy xz yz\n",xy,xz,yz);
// write ff styles to input file
if (fp2) {
fprintf(fp2,"# LAMMPS input file from restart file: "
"timestep = " BIGINT_FORMAT ", procs = %d\n\n",ntimestep,nprocs);
if (pair_style) fprintf(fp2,"pair_style %s\n",pair_style);
if (bond_style) fprintf(fp2,"bond_style %s\n",bond_style);
if (angle_style) fprintf(fp2,"angle_style %s\n",angle_style);
if (dihedral_style) fprintf(fp2,"dihedral_style %s\n",dihedral_style);
if (improper_style) fprintf(fp2,"improper_style %s\n",improper_style);
fprintf(fp2,"special_bonds lj %g %g %g coul %g %g %g\n",
special_lj[1],special_lj[2],special_lj[3],
special_lj[1],special_coul[2],special_coul[3]);
fprintf(fp2,"\n");
}
// mass to both data file and input file for convenience
if (mass) {
if (fp2) {
fprintf(fp2,"\n");
for (int i = 1; i <= ntypes; i++) fprintf(fp2,"mass %d %g\n",i,mass[i]);
fprintf(fp2,"\n");
}
fprintf(fp,"\nMasses\n\n");
for (int i = 1; i <= ntypes; i++) fprintf(fp,"%d %g\n",i,mass[i]);
}
// pair coeffs to data file
if (write_coeffs && pair_style && fp2 == NULL) {
if ((strcmp(pair_style,"none") != 0) &&
(strcmp(pair_style,"adp") != 0) &&
(strcmp(pair_style,"airebo") != 0) &&
(strcmp(pair_style,"brownian") != 0) &&
(strcmp(pair_style,"comb") != 0) &&
(strcmp(pair_style,"coul/cut") != 0) &&
(strcmp(pair_style,"coul/debye") != 0) &&
(strcmp(pair_style,"coul/diel") != 0) &&
(strcmp(pair_style,"coul/long") != 0) &&
(strcmp(pair_style,"eam") != 0) &&
(strcmp(pair_style,"eam/alloy") != 0) &&
(strcmp(pair_style,"eam/fs") != 0) &&
(strcmp(pair_style,"eim") != 0) &&
(strcmp(pair_style,"eff/cut") != 0) &&
(strcmp(pair_style,"gauss") != 0) &&
(strcmp(pair_style,"gauss/cut") != 0) &&
(strcmp(pair_style,"gran/history") != 0) &&
(strcmp(pair_style,"gran/no_history") != 0) &&
(strcmp(pair_style,"gran/hertzian") != 0) &&
(strcmp(pair_style,"lubricate") != 0) &&
(strcmp(pair_style,"lubricateU") != 0) &&
(strcmp(pair_style,"meam") != 0) &&
(strcmp(pair_style,"meam/spline") != 0) &&
(strcmp(pair_style,"rebo") != 0) &&
(strcmp(pair_style,"reax") != 0) &&
(strcmp(pair_style,"reax/c") != 0) &&
(strcmp(pair_style,"sw") != 0) &&
(strcmp(pair_style,"table") != 0) &&
(strcmp(pair_style,"tersoff") != 0) &&
(strcmp(pair_style,"tersoff/table") != 0) &&
(strcmp(pair_style,"tersoff/zbl") != 0) &&
(strcmp(pair_style,"hybrid") != 0) &&
(strcmp(pair_style,"hybrid/overlay") != 0))
fprintf(fp,"\nPair Coeffs\n\n");
if (strcmp(pair_style,"born/coul/long") == 0) {
for (int i = 1; i <= ntypes; i++)
fprintf(fp,"%d %g %g %g %g %g\n",i,
pair_born_A[i],pair_born_rho[i],pair_born_sigma[i],
pair_born_C[i],pair_born_D[i]);
} else if ((strcmp(pair_style,"buck") == 0) ||
(strcmp(pair_style,"buck/coul/cut") == 0) ||
(strcmp(pair_style,"buck/coul/long") == 0) ||
(strcmp(pair_style,"buck/long") == 0)) {
for (int i = 1; i <= ntypes; i++)
fprintf(fp,"%d %g %g %g\n",i,
pair_buck_A[i],pair_buck_rho[i],pair_buck_C[i]);
} else if (strcmp(pair_style,"colloid") == 0) {
for (int i = 1; i <= ntypes; i++)
fprintf(fp,"%d %g %g %g %g\n",i,
pair_colloid_A12[i],pair_colloid_sigma[i],
pair_colloid_d2[i],pair_colloid_d2[i]);
} else if ((strcmp(pair_style,"dipole/cut") == 0) ||
(strcmp(pair_style,"dipole/sf") == 0)) {
for (int i = 1; i <= ntypes; i++)
fprintf(fp,"%d %g %g\n",i,
pair_dipole_epsilon[i],pair_dipole_sigma[i]);
} else if (strcmp(pair_style,"dpd") == 0) {
for (int i = 1; i <= ntypes; i++)
fprintf(fp,"%d %g %g\n",i,
pair_dpd_a0[i],pair_dpd_gamma[i]);
} else if (strcmp(pair_style,"dpd/tstat") == 0) {
for (int i = 1; i <= ntypes; i++)
fprintf(fp,"%d %g\n",i,
pair_dpd_gamma[i]);
} else if (strcmp(pair_style,"gayberne") == 0) {
for (int i = 1; i <= ntypes; i++)
fprintf(fp,"%d %g %g %g %g %g %g %g %g\n",i,
pair_gb_epsilon[i],pair_gb_sigma[i],
pair_gb_epsa[i],pair_gb_epsb[i],pair_gb_epsc[i],
pair_gb_epsa[i],pair_gb_epsb[i],pair_gb_epsc[i]);
} else if ((strcmp(pair_style,"lj/charmm/coul/charmm") == 0) ||
(strcmp(pair_style,"lj/charmm/coul/charmm/implicit") == 0) ||
(strcmp(pair_style,"lj/charmm/coul/long/proxy") == 0) ||
(strcmp(pair_style,"lj/charmm/coul/long") == 0)) {
for (int i = 1; i <= ntypes; i++)
fprintf(fp,"%d %g %g %g %g\n",i,
pair_charmm_epsilon[i],pair_charmm_sigma[i],
pair_charmm_eps14[i],pair_charmm_sigma14[i]);
} else if ((strcmp(pair_style,"lj/class2") == 0) ||
(strcmp(pair_style,"lj/class2/coul/cut") == 0) ||
(strcmp(pair_style,"lj/class2/coul/long/proxy") == 0) ||
(strcmp(pair_style,"lj/class2/coul/long") == 0)) {
for (int i = 1; i <= ntypes; i++)
fprintf(fp,"%d %g %g\n",i,
pair_class2_epsilon[i],pair_class2_sigma[i]);
} else if ((strcmp(pair_style,"lj/cut") == 0) ||
(strcmp(pair_style,"lj96/cut") == 0) ||
(strcmp(pair_style,"lj/cut/coul/cut") == 0) ||
(strcmp(pair_style,"lj/cut/coul/debye") == 0) ||
(strcmp(pair_style,"lj/cut/coul/long") == 0) ||
(strcmp(pair_style,"lj/cut/coul/long/proxy") == 0) ||
(strcmp(pair_style,"lj/cut/tip4p/cut") == 0) ||
(strcmp(pair_style,"lj/cut/tip4p/long") == 0) ||
(strcmp(pair_style,"lj/long/coul/long") == 0)) {
for (int i = 1; i <= ntypes; i++)
fprintf(fp,"%d %g %g\n",i,
pair_lj_epsilon[i],pair_lj_sigma[i]);
} else if (strcmp(pair_style,"lj/expand") == 0) {
for (int i = 1; i <= ntypes; i++)
fprintf(fp,"%d %g %g %g\n",i,
pair_ljexpand_epsilon[i],pair_ljexpand_sigma[i],
pair_ljexpand_shift[i]);
} else if ((strcmp(pair_style,"lj/gromacs") == 0) ||
(strcmp(pair_style,"lj/gromacs/coul/gromacs") == 0)) {
for (int i = 1; i <= ntypes; i++)
fprintf(fp,"%d %g %g\n",i,
pair_ljgromacs_epsilon[i],pair_ljgromacs_sigma[i]);
} else if (strcmp(pair_style,"lj/smooth") == 0) {
for (int i = 1; i <= ntypes; i++)
fprintf(fp,"%d %g %g\n",i,
pair_ljsmooth_epsilon[i],pair_ljsmooth_sigma[i]);
} else if (strcmp(pair_style,"morse") == 0) {
for (int i = 1; i <= ntypes; i++)
fprintf(fp,"%d %g %g %g\n",i,
pair_morse_d0[i],pair_morse_alpha[i],pair_morse_r0[i]);
} else if (strcmp(pair_style,"soft") == 0) {
for (int i = 1; i <= ntypes; i++)
fprintf(fp,"%d %g\n",i,
pair_soft_A[i]);
} else if ((strcmp(pair_style,"yukawa") == 0) ||
(strcmp(pair_style,"yukawa/colloid") == 0)) {
for (int i = 1; i <= ntypes; i++)
fprintf(fp,"%d %g\n",i,
pair_yukawa_A[i]);
} else if ((strcmp(pair_style,"cg/cmm") == 0) ||
(strcmp(pair_style,"cg/cmm/coul/cut") == 0) ||
(strcmp(pair_style,"cg/cmm/coul/long") == 0) ||
(strcmp(pair_style,"lj/sdk") == 0) ||
(strcmp(pair_style,"lj/sdk/coul/long") == 0)) {
printf("ERROR: Cannot write pair_style %s to data file alone. please provide an input file, too.\n",
pair_style);
exit(1);
}
}
// pair coeffs to input file
// only supported styles = lj/sdk and cg/cmm
if (write_coeffs && pair_style && fp2) {
if ((strcmp(pair_style,"lj/sdk") == 0) ||
(strcmp(pair_style,"lj/sdk/coul/long") == 0) ||
(strcmp(pair_style,"cg/cmm") == 0) ||
(strcmp(pair_style,"cg/cmm/coul/cut") == 0) ||
(strcmp(pair_style,"cg/cmm/old") == 0) ||
(strcmp(pair_style,"cg/cmm/coul/cut/old") == 0) ||
(strcmp(pair_style,"cg/cmm/coul/long/old") == 0)) {
for (int i = 1; i <= ntypes; i++) {
for (int j = i; j <= ntypes; j++) {
fprintf(fp2,"pair_coeff %d %d %s %g %g\n",i,j,
cg_type_list[pair_cg_cmm_type[i][j]],
pair_cg_epsilon[i][j],pair_cg_sigma[i][j]);
}
}
} else {
printf("ERROR: Cannot write pair_style %s to input file\n",
pair_style);
exit(1);
}
}
// bond coeffs to data file
if (write_coeffs && bond_style && fp2 == NULL) {
if ((strcmp(bond_style,"none") != 0) &&
(strcmp(bond_style,"table") != 0) &&
(strcmp(bond_style,"hybrid") != 0))
fprintf(fp,"\nBond Coeffs\n\n");
if (strcmp(bond_style,"class2") == 0) {
for (int i = 1; i <= nbondtypes; i++)
fprintf(fp,"%d %g %g %g %g\n",i,
bond_class2_r0[i],bond_class2_k2[i],
bond_class2_k3[i],bond_class2_k4[i]);
} else if (strcmp(bond_style,"fene") == 0) {
for (int i = 1; i <= nbondtypes; i++)
fprintf(fp,"%d %g %g %g %g\n",i,
bond_fene_k[i],bond_fene_r0[i],
bond_fene_epsilon[i],bond_fene_sigma[i]);
} else if (strcmp(bond_style,"fene/expand") == 0) {
for (int i = 1; i <= nbondtypes; i++)
fprintf(fp,"%d %g %g %g %g %g\n",i,
bond_feneexpand_k[i],bond_feneexpand_r0[i],
bond_feneexpand_epsilon[i],bond_feneexpand_sigma[i],
bond_feneexpand_shift[i]);
} else if (strcmp(bond_style,"harmonic") == 0) {
for (int i = 1; i <= nbondtypes; i++)
fprintf(fp,"%d %g %g\n",i,
bond_harmonic_k[i],bond_harmonic_r0[i]);
} else if (strcmp(bond_style,"harmonicshift") == 0) {
for (int i = 1; i <= nbondtypes; i++)
fprintf(fp,"%d %g %g %g\n",i,
bond_harmonicshift_umin[i],bond_harmonicshift_r0[i],
bond_harmonicshift_rc[i]);
} else if (strcmp(bond_style,"harmonicshiftcut") == 0) {
for (int i = 1; i <= nbondtypes; i++)
fprintf(fp,"%d %g %g %g\n",i,
bond_harmonicshiftcut_umin[i],bond_harmonicshiftcut_r0[i],
bond_harmonicshiftcut_rc[i]);
} else if (strcmp(bond_style,"morse") == 0) {
for (int i = 1; i <= nbondtypes; i++)
fprintf(fp,"%d %g %g %g\n",i,
bond_morse_d0[i],bond_morse_alpha[i],bond_morse_r0[i]);
} else if (strcmp(bond_style,"nonlinear") == 0) {
for (int i = 1; i <= nbondtypes; i++)
fprintf(fp,"%d %g %g %g\n",i,
bond_nonlinear_epsilon[i],bond_nonlinear_r0[i],
bond_nonlinear_lamda[i]);
} else if (strcmp(bond_style,"quartic") == 0) {
for (int i = 1; i <= nbondtypes; i++)
fprintf(fp,"%d %g %g %g %g %g\n",i,
bond_quartic_k[i],bond_quartic_b1[i],bond_quartic_b2[i],
bond_quartic_rc[i],bond_quartic_u0[i]);
}
}
// bond coeffs to input file
// only supported styles = harmonic
if (write_coeffs && bond_style && fp2) {
if (strcmp(bond_style,"harmonic") == 0) {
for (int i = 1; i <= nbondtypes; i++)
fprintf(fp2,"bond_coeff %d %g %g\n",i,
bond_harmonic_k[i],bond_harmonic_r0[i]);
} else {
printf("ERROR: Cannot write bond_style %s to input file\n",
bond_style);
exit(1);
}
}
// angle coeffs to data file
if (write_coeffs && angle_style && fp2 == NULL) {
if ((strcmp(angle_style,"none") != 0) &&
(strcmp(angle_style,"table") != 0) &&
(strcmp(angle_style,"hybrid") != 0))
fprintf(fp,"\nAngle Coeffs\n\n");
if (strcmp(angle_style,"charmm") == 0) {
for (int i = 1; i <= nangletypes; i++)
fprintf(fp,"%d %g %g %g %g\n",i,
angle_charmm_k[i],angle_charmm_theta0[i]/PI*180.0,
angle_charmm_k_ub[i],angle_charmm_r_ub[i]);
} else if (strcmp(angle_style,"class2") == 0) {
for (int i = 1; i <= nangletypes; i++)
fprintf(fp,"%d %g %g %g %g\n",i,
angle_class2_theta0[i]/PI*180.0,angle_class2_k2[i],
angle_class2_k3[i],angle_class2_k4[i]);
fprintf(fp,"\nBondBond Coeffs\n\n");
for (int i = 1; i <= nangletypes; i++)
fprintf(fp,"%d %g %g %g\n",i,
angle_class2_bb_k[i],
angle_class2_bb_r1[i],angle_class2_bb_r2[i]);
fprintf(fp,"\nBondAngle Coeffs\n\n");
for (int i = 1; i <= nangletypes; i++)
fprintf(fp,"%d %g %g %g %g\n",i,
angle_class2_ba_k1[i],angle_class2_ba_k2[i],
angle_class2_ba_r1[i],angle_class2_ba_r2[i]);
} else if (strcmp(angle_style,"cosine") == 0) {
for (int i = 1; i <= nangletypes; i++)
fprintf(fp,"%d %g\n",i,angle_cosine_k[i]);
} else if (strcmp(angle_style,"cosineshift") == 0) {
for (int i = 1; i <= nangletypes; i++)
fprintf(fp,"%d %g %g\n",i,angle_cosineshift_umin[i],
angle_cosineshift_theta0[i]/PI*180.0);
} else if (strcmp(angle_style,"cosineshiftexp") == 0) {
for (int i = 1; i <= nangletypes; i++)
fprintf(fp,"%d %g %g %g\n",i,angle_cosineshiftexp_umin[i],
angle_cosineshiftexp_theta0[i]/PI*180.0,
angle_cosineshiftexp_a[i]);
} else if ((strcmp(angle_style,"cosine/squared") == 0) ||
(strcmp(angle_style,"cosine/delta") == 0)) {
for (int i = 1; i <= nangletypes; i++)
fprintf(fp,"%d %g %g\n",i,
angle_cosine_squared_k[i],
angle_cosine_squared_theta0[i]/PI*180.0);
} else if (strcmp(angle_style,"dipole") == 0) {
for (int i = 1; i <= nangletypes; i++)
fprintf(fp,"%d %g %g\n",i,
angle_harmonic_k[i],angle_harmonic_theta0[i]/PI*180.0);
} else if (strcmp(angle_style,"harmonic") == 0) {
for (int i = 1; i <= nangletypes; i++)
fprintf(fp,"%d %g %g\n",i,
angle_harmonic_k[i],angle_harmonic_theta0[i]/PI*180.0);
} else if ((strcmp(angle_style,"cg/cmm") == 0) ||
(strcmp(angle_style,"sdk") == 0)) {
for (int i = 1; i <= nangletypes; i++)
fprintf(fp,"%d %g %g %g\n",i,angle_harmonic_k[i],
angle_harmonic_theta0[i]/PI*180.0,angle_cg_cmm_epsilon[i]);
} else if (strcmp(angle_style,"cg/cmm/old") == 0) {
for (int i = 1; i <= nangletypes; i++)
fprintf(fp,"%d %g %g %s %g %g\n",i,
angle_harmonic_k[i],angle_harmonic_theta0[i]/PI*180.0,
cg_type_list[angle_cg_cmm_type[i]],angle_cg_cmm_epsilon[i],
angle_cg_cmm_sigma[i]);
}
}
// angle coeffs to input file
// only supported styles = cosine/squared, harmonic, cg/cmm
if (write_coeffs && angle_style && fp2) {
if ((strcmp(angle_style,"cosine/squared") == 0) ||
(strcmp(angle_style,"cosine/delta") == 0)) {
for (int i = 1; i <= nangletypes; i++)
fprintf(fp2,"angle_coeffs %d %g %g\n",i,
angle_cosine_squared_k[i],
angle_cosine_squared_theta0[i]/PI*180.0);
} else if (strcmp(angle_style,"harmonic") == 0) {
for (int i = 1; i <= nangletypes; i++)
fprintf(fp2,"angle_coeffs %d %g %g\n",i,
angle_harmonic_k[i],angle_harmonic_theta0[i]/PI*180.0);
} else if ((strcmp(angle_style,"cg/cmm") == 0) ||
(strcmp(angle_style,"sdk") == 0)) {
for (int i = 1; i <= nangletypes; i++)
fprintf(fp2,"angle_coeffs %d %g %g %g\n",i,angle_harmonic_k[i],
angle_harmonic_theta0[i]/PI*180.0,angle_cg_cmm_epsilon[i]);
} else if (strcmp(angle_style,"cg/cmm/old") == 0) {
for (int i = 1; i <= nangletypes; i++)
fprintf(fp2,"angle_coeffs %d %g %g %s %g %g\n",i,
angle_harmonic_k[i],angle_harmonic_theta0[i]/PI*180.0,
cg_type_list[angle_cg_cmm_type[i]],angle_cg_cmm_epsilon[i],
angle_cg_cmm_sigma[i]);
} else {
printf("ERROR: Cannot write angle_style %s to input file\n",
angle_style);
exit(1);
}
}
if (write_coeffs && dihedral_style) {
if ((strcmp(dihedral_style,"none") != 0) &&
(strcmp(dihedral_style,"table") != 0) &&
(strcmp(dihedral_style,"hybrid") != 0))
fprintf(fp,"\nDihedral Coeffs\n\n");
if (strcmp(dihedral_style,"charmm") == 0) {
for (int i = 1; i <= ndihedraltypes; i++)
fprintf(fp,"%d %g %d %d %g\n",i,
dihedral_charmm_k[i],dihedral_charmm_multiplicity[i],
dihedral_charmm_sign[i],dihedral_charmm_weight[i]);
} else if (strcmp(dihedral_style,"class2") == 0) {
for (int i = 1; i <= ndihedraltypes; i++)
fprintf(fp,"%d %g %g %g %g %g %g\n",i,
dihedral_class2_k1[i],
dihedral_class2_phi1[i]/PI*180.0,
dihedral_class2_k2[i],
dihedral_class2_phi2[i]/PI*180.0,
dihedral_class2_k3[i],
dihedral_class2_phi3[i]/PI*180.0);
fprintf(fp,"\nMiddleBondTorsion Coeffs\n\n");
for (int i = 1; i <= ndihedraltypes; i++)
fprintf(fp,"%d %g %g %g %g\n",i,
dihedral_class2_mbt_f1[i],dihedral_class2_mbt_f2[i],
dihedral_class2_mbt_f3[i],dihedral_class2_mbt_r0[i]);
fprintf(fp,"\nEndBondTorsion Coeffs\n\n");
for (int i = 1; i <= ndihedraltypes; i++)
fprintf(fp,"%d %g %g %g %g %g %g %g %g\n",i,
dihedral_class2_ebt_f1_1[i],dihedral_class2_ebt_f2_1[i],
dihedral_class2_ebt_f3_1[i],
dihedral_class2_ebt_f1_2[i],dihedral_class2_ebt_f2_2[i],
dihedral_class2_ebt_f3_2[i],
dihedral_class2_ebt_r0_1[i],
dihedral_class2_ebt_r0_2[i]);
fprintf(fp,"\nAngleTorsion Coeffs\n\n");
for (int i = 1; i <= ndihedraltypes; i++)
fprintf(fp,"%d %g %g %g %g %g %g %g %g\n",i,
dihedral_class2_at_f1_1[i],dihedral_class2_at_f2_1[i],
dihedral_class2_at_f3_1[i],
dihedral_class2_at_f1_2[i],dihedral_class2_at_f2_2[i],
dihedral_class2_at_f3_2[i],
dihedral_class2_at_theta0_1[i]/PI*180.0,
dihedral_class2_at_theta0_2[i]/PI*180.0);
fprintf(fp,"\nAngleAngleTorsion Coeffs\n\n");
for (int i = 1; i <= ndihedraltypes; i++)
fprintf(fp,"%d %g %g %g\n",i,
dihedral_class2_aat_k[i],
dihedral_class2_aat_theta0_1[i]/PI*180.0,
dihedral_class2_aat_theta0_2[i]/PI*180.0);
fprintf(fp,"\nBondBond13 Coeffs\n\n");
for (int i = 1; i <= ndihedraltypes; i++)
fprintf(fp,"%d %g %g %g\n",i,
dihedral_class2_bb13_k[i],
dihedral_class2_bb13_r10[i],dihedral_class2_bb13_r30[i]);
} else if (strcmp(dihedral_style,"harmonic") == 0) {
for (int i = 1; i <= ndihedraltypes; i++)
fprintf(fp,"%d %g %d %d\n",i,
dihedral_harmonic_k[i],dihedral_harmonic_multiplicity[i],
dihedral_harmonic_sign[i]);
} else if (strcmp(dihedral_style,"cosineshiftexp") == 0) {
for (int i = 1; i <= ndihedraltypes; i++)
fprintf(fp,"%d %g %g %g\n",i,
dihedral_cosineshiftexp_umin[i],
dihedral_cosineshiftexp_theta[i]*180.0/PI,
dihedral_cosineshiftexp_a[i]
);
} else if (strcmp(dihedral_style,"helix") == 0) {
for (int i = 1; i <= ndihedraltypes; i++)
fprintf(fp,"%d %g %g %g\n",i,dihedral_helix_aphi[i],
dihedral_helix_bphi[i],dihedral_helix_cphi[i]);
} else if (strcmp(dihedral_style,"multi/harmonic") == 0) {
for (int i = 1; i <= ndihedraltypes; i++)
fprintf(fp,"%d %g %g %g %g %g\n",i,
dihedral_multi_a1[i],dihedral_multi_a2[i],
dihedral_multi_a3[i],dihedral_multi_a4[i],
dihedral_multi_a5[i]);
} else if (strcmp(dihedral_style,"opls") == 0) {
for (int i = 1; i <= ndihedraltypes; i++) // restore factor of 2
fprintf(fp,"%d %g %g %g %g\n",i,
2.0*dihedral_opls_k1[i],2.0*dihedral_opls_k2[i],
2.0*dihedral_opls_k3[i],2.0*dihedral_opls_k4[i]);
}
}
if (write_coeffs && improper_style) {
if ((strcmp(improper_style,"none") != 0) &&
(strcmp(improper_style,"hybrid") != 0))
fprintf(fp,"\nImproper Coeffs\n\n");
if (strcmp(improper_style,"class2") == 0) {
for (int i = 1; i <= nimpropertypes; i++)
fprintf(fp,"%d %g %g\n",i,
improper_class2_k0[i],improper_class2_chi0[i]/PI*180.0);
fprintf(fp,"\nAngleAngle Coeffs\n\n");
for (int i = 1; i <= nimpropertypes; i++)
fprintf(fp,"%d %g %g %g %g %g %g\n",i,
improper_class2_aa_k1[i],improper_class2_aa_k2[i],
improper_class2_aa_k3[i],
improper_class2_aa_theta0_1[i]/PI*180.0,
improper_class2_aa_theta0_2[i]/PI*180.0,
improper_class2_aa_theta0_3[i]/PI*180.0);
} else if (strcmp(improper_style,"cvff") == 0) {
for (int i = 1; i <= nimpropertypes; i++)
fprintf(fp,"%d %g %d %d\n",i,
improper_cvff_k[i],improper_cvff_sign[i],
improper_cvff_multiplicity[i]);
} else if (strcmp(improper_style,"harmonic") == 0) {
for (int i = 1; i <= nimpropertypes; i++)
fprintf(fp,"%d %g %g\n",i,
improper_harmonic_k[i],improper_harmonic_chi[i]/PI*180.0);
}
}
if (natoms) {
fprintf(fp,"\nAtoms\n\n");
int ix,iy,iz;
for (bigint i = 0; i < natoms; i++) {
ix = (image[i] & IMGMASK) - IMGMAX;
iy = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
iz = (image[i] >> IMG2BITS) - IMGMAX;
if (style_hybrid == 0) {
if (style_angle) write_atom_angle(fp,i,ix,iy,iz);
if (style_atomic) write_atom_atomic(fp,i,ix,iy,iz);
if (style_bond) write_atom_bond(fp,i,ix,iy,iz);
if (style_charge) write_atom_charge(fp,i,ix,iy,iz);
if (style_dipole) write_atom_dipole(fp,i,ix,iy,iz);
if (style_ellipsoid) write_atom_ellipsoid(fp,i,ix,iy,iz);
if (style_full) write_atom_full(fp,i,ix,iy,iz);
if (style_line) write_atom_line(fp,i,ix,iy,iz);
if (style_meso) write_atom_meso(fp,i,ix,iy,iz);
if (style_molecular) write_atom_molecular(fp,i,ix,iy,iz);
if (style_peri) write_atom_peri(fp,i,ix,iy,iz);
if (style_sphere) write_atom_sphere(fp,i,ix,iy,iz);
if (style_tri) write_atom_tri(fp,i,ix,iy,iz);
if (style_wavepacket) write_atom_wavepacket(fp,i,ix,iy,iz);
fprintf(fp,"\n");
} else {
fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e",
tag[i],type[i],x[i],y[i],z[i]);
for (int k = 1; k <= style_hybrid; k++) {
if (k == style_angle) write_atom_angle_extra(fp,i);
if (k == style_atomic) write_atom_atomic_extra(fp,i);
if (k == style_bond) write_atom_bond_extra(fp,i);
if (k == style_charge) write_atom_charge_extra(fp,i);
if (k == style_dipole) write_atom_dipole_extra(fp,i);
if (k == style_ellipsoid) write_atom_ellipsoid_extra(fp,i);
if (k == style_full) write_atom_full_extra(fp,i);
if (k == style_line) write_atom_line_extra(fp,i);
if (k == style_meso) write_atom_meso_extra(fp,i);
if (k == style_molecular) write_atom_molecular_extra(fp,i);
if (k == style_peri) write_atom_peri_extra(fp,i);
if (k == style_sphere) write_atom_sphere_extra(fp,i);
if (k == style_tri) write_atom_tri_extra(fp,i);
if (k == style_wavepacket) write_atom_wavepacket_extra(fp,i);
}
fprintf(fp," %d %d %d\n",ix,iy,iz);
}
}
}
if (write_vels && natoms) {
fprintf(fp,"\nVelocities\n\n");
for (bigint i = 0; i < natoms; i++)
if (style_hybrid == 0) {
if (style_angle) write_vel_angle(fp,i);
if (style_atomic) write_vel_atomic(fp,i);
if (style_bond) write_vel_bond(fp,i);
if (style_charge) write_vel_charge(fp,i);
if (style_dipole) write_vel_dipole(fp,i);
if (style_ellipsoid) write_vel_ellipsoid(fp,i);
if (style_full) write_vel_full(fp,i);
if (style_line) write_vel_line(fp,i);
if (style_meso) write_vel_meso(fp,i);
if (style_molecular) write_vel_molecular(fp,i);
if (style_peri) write_vel_peri(fp,i);
if (style_sphere) write_vel_sphere(fp,i);
if (style_tri) write_vel_tri(fp,i);
if (style_wavepacket) write_vel_wavepacket(fp,i);
fprintf(fp,"\n");
} else {
fprintf(fp,"%d %-1.16e %-1.16e %-1.16e",tag[i],vx[i],vy[i],vz[i]);
for (int k = 1; k <= style_hybrid; k++) {
if (k == style_angle) write_vel_angle_extra(fp,i);
if (k == style_atomic) write_vel_atomic_extra(fp,i);
if (k == style_bond) write_vel_bond_extra(fp,i);
if (k == style_charge) write_vel_charge_extra(fp,i);
if (k == style_dipole) write_vel_dipole_extra(fp,i);
if (k == style_ellipsoid) write_vel_ellipsoid_extra(fp,i);
if (k == style_full) write_vel_full_extra(fp,i);
if (k == style_line) write_vel_line_extra(fp,i);
if (k == style_meso) write_vel_meso_extra(fp,i);
if (k == style_molecular) write_vel_molecular_extra(fp,i);
if (k == style_peri) write_vel_peri_extra(fp,i);
if (k == style_sphere) write_vel_sphere_extra(fp,i);
if (k == style_tri) write_vel_tri_extra(fp,i);
if (k == style_wavepacket) write_vel_wavepacket_extra(fp,i);
}
fprintf(fp,"\n");
}
}
if (nellipsoids) {
fprintf(fp,"\nEllipsoids\n\n");
for (bigint i = 0; i < natoms; i++) {
if (ellipsoid[i])
fprintf(fp,"%d %-1.16e %-1.16e %-1.16e "
"%-1.16e %-1.16e %-1.16e %-1.16e \n",
tag[i],2.0*shapex[i],2.0*shapey[i],2.0*shapez[i],
quatw[i],quati[i],quatj[i],quatk[i]);
}
}
if (ibonds) {
fprintf(fp,"\nBonds\n\n");
for (bigint i = 0; i < ibonds; i++)
fprintf(fp,BIGINT_FORMAT " %d %d %d\n",
i+1,bond_type[i],bond_atom1[i],bond_atom2[i]);
}
if (iangles) {
fprintf(fp,"\nAngles\n\n");
for (bigint i = 0; i < iangles; i++)
fprintf(fp,BIGINT_FORMAT " %d %d %d %d\n",
i+1,angle_type[i],angle_atom1[i],angle_atom2[i],angle_atom3[i]);
}
if (idihedrals) {
fprintf(fp,"\nDihedrals\n\n");
for (bigint i = 0; i < idihedrals; i++)
fprintf(fp,BIGINT_FORMAT " %d %d %d %d %d\n",
i+1,dihedral_type[i],dihedral_atom1[i],dihedral_atom2[i],
dihedral_atom3[i],dihedral_atom4[i]);
}
if (iimpropers) {
fprintf(fp,"\nImpropers\n\n");
for (bigint i = 0; i < iimpropers; i++)
fprintf(fp,BIGINT_FORMAT " %d %d %d %d %d\n",
i+1,improper_type[i],improper_atom1[i],improper_atom2[i],
improper_atom3[i],improper_atom4[i]);
}
}
// ---------------------------------------------------------------------
// per-atom write routines
// one routine per atom style
// ---------------------------------------------------------------------
void Data::write_atom_angle(FILE *fp, int i, int ix, int iy, int iz)
{
fprintf(fp,"%d %d %d %-1.16e %-1.16e %-1.16e %d %d %d",
tag[i],molecule[i],type[i],x[i],y[i],z[i],ix,iy,iz);
}
void Data::write_atom_atomic(FILE *fp, int i, int ix, int iy, int iz)
{
fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %d %d %d",
tag[i],type[i],x[i],y[i],z[i],ix,iy,iz);
}
void Data::write_atom_bond(FILE *fp, int i, int ix, int iy, int iz)
{
fprintf(fp,"%d %d %d %-1.16e %-1.16e %-1.16e %d %d %d",
tag[i],molecule[i],type[i],x[i],y[i],z[i],ix,iy,iz);
}
void Data::write_atom_charge(FILE *fp, int i, int ix, int iy, int iz)
{
fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d",
tag[i],type[i],q[i],x[i],y[i],z[i],ix,iy,iz);
}
void Data::write_atom_dipole(FILE *fp, int i, int ix, int iy, int iz)
{
fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e "
"%-1.16e %-1.16e %d %d %d",
tag[i],type[i],q[i],x[i],y[i],z[i],
mul[i]*mux[i],mul[i]*muy[i],mul[i]*muz[i],
ix,iy,iz);
}
void Data::write_atom_ellipsoid(FILE *fp, int i, int ix, int iy, int iz)
{
fprintf(fp,"%d %d %d %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d",
tag[i],type[i],ellipsoid[i],density[i],x[i],y[i],z[i],ix,iy,iz);
}
void Data::write_atom_full(FILE *fp, int i, int ix, int iy, int iz)
{
fprintf(fp,"%d %d %d %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d",
tag[i],molecule[i],type[i],q[i],x[i],y[i],z[i],ix,iy,iz);
}
void Data::write_atom_line(FILE *fp, int i, int ix, int iy, int iz)
{
fprintf(stderr,"support for atom style line is not yet complete\n");
exit(1);
}
void Data::write_atom_meso(FILE *fp, int i, int ix, int iy, int iz)
{
fprintf(stderr,"support for atom style meso is not yet complete\n");
exit(1);
}
void Data::write_atom_molecular(FILE *fp, int i, int ix, int iy, int iz)
{
fprintf(fp,"%d %d %d %-1.16e %-1.16e %-1.16e %d %d %d",
tag[i],molecule[i],type[i],x[i],y[i],z[i],ix,iy,iz);
}
void Data::write_atom_peri(FILE *fp, int i, int ix, int iy, int iz)
{
fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d",
tag[i],type[i],vfrac[i],rmass[i],x[i],y[i],z[i],ix,iy,iz);
}
void Data::write_atom_sphere(FILE *fp, int i, int ix, int iy, int iz)
{
fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d",
tag[i],type[i],2.0*radius[i],density[i],x[i],y[i],z[i],ix,iy,iz);
}
void Data::write_atom_tri(FILE *fp, int i, int ix, int iy, int iz)
{
fprintf(stderr,"support for atom style tri is not yet complete\n");
exit(1);
}
void Data::write_atom_wavepacket(FILE *fp, int i, int ix, int iy, int iz)
{
fprintf(stderr,"support for atom style wavepacket is not yet complete\n");
exit(1);
}
// ---------------------------------------------------------------------
// per-atom write routines of extra quantities unique to style
// one routine per atom style
// ---------------------------------------------------------------------
void Data::write_atom_angle_extra(FILE *fp, int i)
{
fprintf(fp," %d",molecule[i]);
}
void Data::write_atom_atomic_extra(FILE *fp, int i) {}
void Data::write_atom_bond_extra(FILE *fp, int i)
{
fprintf(fp," %d",molecule[i]);
}
void Data::write_atom_charge_extra(FILE *fp, int i)
{
fprintf(fp," %-1.16e",q[i]);
}
void Data::write_atom_dipole_extra(FILE *fp, int i)
{
fprintf(fp," %-1.16e %-1.16e %-1.16e %-1.16e",q[i],
mul[i]*mux[i],mul[i]*muy[i],mul[i]*muz[i]);
}
void Data::write_atom_ellipsoid_extra(FILE *fp, int i)
{
fprintf(fp," %d %-1.16e",ellipsoid[i],density[i]);
}
void Data::write_atom_full_extra(FILE *fp, int i)
{
fprintf(fp," %d %-1.16e",molecule[i],q[i]);
}
void Data::write_atom_line_extra(FILE *fp, int i)
{
fprintf(stderr,"support for atom style line is not yet complete\n");
exit(1);
}
void Data::write_atom_meso_extra(FILE *fp, int i)
{
fprintf(stderr,"support for atom style meso is not yet complete\n");
exit(1);
}
void Data::write_atom_molecular_extra(FILE *fp, int i)
{
fprintf(fp," %d",molecule[i]);
}
void Data::write_atom_peri_extra(FILE *fp, int i)
{
fprintf(fp," %-1.16e %-1.16e",vfrac[i],rmass[i]);
}
void Data::write_atom_sphere_extra(FILE *fp, int i)
{
fprintf(fp," %-1.16e %-1.16e",2.0*radius[i],density[i]);
}
void Data::write_atom_tri_extra(FILE *fp, int i)
{
fprintf(stderr,"support for atom style tri is not yet complete\n");
exit(1);
}
void Data::write_atom_wavepacket_extra(FILE *fp, int i)
{
fprintf(stderr,"support for atom style wavepacket is not yet complete\n");
exit(1);
}
// ---------------------------------------------------------------------
// per-atom velocity write routines
// one routine per atom style
// ---------------------------------------------------------------------
void Data::write_vel_angle(FILE *fp, int i)
{
fprintf(fp,"%d %-1.16e %-1.16e %-1.16e",tag[i],vx[i],vy[i],vz[i]);
}
void Data::write_vel_atomic(FILE *fp, int i)
{
fprintf(fp,"%d %-1.16e %-1.16e %-1.16e",tag[i],vx[i],vy[i],vz[i]);
}
void Data::write_vel_bond(FILE *fp, int i)
{
fprintf(fp,"%d %-1.16e %-1.16e %-1.16e",tag[i],vx[i],vy[i],vz[i]);
}
void Data::write_vel_charge(FILE *fp, int i)
{
fprintf(fp,"%d %-1.16e %-1.16e %-1.16e",tag[i],vx[i],vy[i],vz[i]);
}
void Data::write_vel_dipole(FILE *fp, int i)
{
fprintf(fp,"%d %-1.16e %-1.16e %-1.16e",tag[i],vx[i],vy[i],vz[i]);
}
void Data::write_vel_ellipsoid(FILE *fp, int i)
{
fprintf(fp,"%d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e",
tag[i],vx[i],vy[i],vz[i],angmomx[i],angmomy[i],angmomz[i]);
}
void Data::write_vel_full(FILE *fp, int i)
{
fprintf(fp,"%d %-1.16e %-1.16e %-1.16e",tag[i],vx[i],vy[i],vz[i]);
}
void Data::write_vel_line(FILE *fp, int i)
{
fprintf(stderr,"support for atom style line is not yet complete\n");
exit(1);
}
void Data::write_vel_meso(FILE *fp, int i)
{
fprintf(stderr,"support for atom style meso is not yet complete\n");
exit(1);
}
void Data::write_vel_molecular(FILE *fp, int i)
{
fprintf(fp,"%d %-1.16e %-1.16e %-1.16e",tag[i],vx[i],vy[i],vz[i]);
}
void Data::write_vel_peri(FILE *fp, int i)
{
fprintf(fp,"%d %-1.16e %-1.16e %-1.16e",tag[i],vx[i],vy[i],vz[i]);
}
void Data::write_vel_sphere(FILE *fp, int i)
{
fprintf(fp,"%d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e",
tag[i],vx[i],vy[i],vz[i],omegax[i],omegay[i],omegaz[i]);
}
void Data::write_vel_tri(FILE *fp, int i)
{
fprintf(stderr,"support for atom style tri is not yet complete\n");
exit(1);
}
void Data::write_vel_wavepacket(FILE *fp, int i)
{
fprintf(stderr,"support for atom style wavepacket is not yet complete\n");
exit(1);
}
// ---------------------------------------------------------------------
// per-atom velocity write routines of extra quantities unique to style
// one routine per atom style
// ---------------------------------------------------------------------
void Data::write_vel_angle_extra(FILE *fp, int i) {}
void Data::write_vel_atomic_extra(FILE *fp, int i) {}
void Data::write_vel_bond_extra(FILE *fp, int i) {}
void Data::write_vel_charge_extra(FILE *fp, int i) {}
void Data::write_vel_dipole_extra(FILE *fp, int i) {}
void Data::write_vel_ellipsoid_extra(FILE *fp, int i)
{
fprintf(fp," %-1.16e %-1.16e %-1.16e",angmomx[i],angmomy[i],angmomz[i]);
}
void Data::write_vel_full_extra(FILE *fp, int i) {}
void Data::write_vel_line_extra(FILE *fp, int i) {}
void Data::write_vel_meso_extra(FILE *fp, int i) {}
void Data::write_vel_molecular_extra(FILE *fp, int i) {}
void Data::write_vel_peri_extra(FILE *fp, int i) {}
void Data::write_vel_sphere_extra(FILE *fp, int i)
{
fprintf(fp," %-1.16e %-1.16e %-1.16e",omegax[i],omegay[i],omegaz[i]);
}
void Data::write_vel_tri_extra(FILE *fp, int i) {}
void Data::write_vel_wavepacket_extra(FILE *fp, int i) {}
// ---------------------------------------------------------------------
// strip known accelerator suffixes from style name
// ---------------------------------------------------------------------
void strip_suffix(char *style)
{
char *slash = strrchr(style,'/');
if (slash == NULL) return;
int i=0;
const char *suffix_list[] = { "/opt", "/gpu", "/cuda", "/omp", NULL };
const char *suffix = suffix_list[0];
while (suffix != NULL) {
if (strcmp(slash,suffix) == 0) {
*slash = '\0';
return;
}
++i;
suffix = suffix_list[i];
}
}
// ---------------------------------------------------------------------
// binary reads from restart file
// all are wrappers on fread()
// perform endian swap if swapflag is set
// ---------------------------------------------------------------------
void nread_int(int *buf, int n, FILE *fp)
{
fread(buf,sizeof(int),n,fp);
if (swapflag) {}
}
void nread_double(double *buf, int n, FILE *fp)
{
fread(buf,sizeof(double),n,fp);
if (swapflag) {}
}
int read_int(FILE *fp)
{
int value;
fread(&value,sizeof(int),1,fp);
if (swapflag) {}
return value;
}
double read_double(FILE *fp)
{
double value;
fread(&value,sizeof(double),1,fp);
if (swapflag) {}
return value;
}
char *read_char(FILE *fp)
{
int n;
fread(&n,sizeof(int),1,fp);
if (swapflag) {}
if (n == 0) return NULL;
char *value = new char[n];
fread(value,sizeof(char),n,fp);
if (swapflag) {}
return value;
}
bigint read_bigint(FILE *fp)
{
bigint value;
fread(&value,sizeof(bigint),1,fp);
if (swapflag) {}
return value;
}
// ---------------------------------------------------------------------
// auto-detect if restart file needs to be byte-swapped on this platform
// return 0 if not, 1 if it does
// re-open file with fp after checking first few bytes
// ---------------------------------------------------------------------
int autodetect(FILE **pfp, char *file)
{
FILE *fp = *pfp;
// read, check, set return flag
int flag = 0;
// reset file pointer
fclose(fp);
fp = fopen(file,"rb");
*pfp = fp;
return flag;
}

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