diff --git a/tools/restart2data.cpp b/tools/restart2data.cpp index 7d5317bd3..f561f2233 100644 --- a/tools/restart2data.cpp +++ b/tools/restart2data.cpp @@ -1,3361 +1,3367 @@ /* ----------------------------------------------------------------------- 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) // 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 // same as write_restart.cpp enum{VERSION,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,SHAPE,DIPOLE}; enum{PAIR,BOND,ANGLE,DIHEDRAL,IMPROPER}; static const char * const cg_type_list[] = {"none", "lj9_6", "lj12_4", "lj12_6"}; // --------------------------------------------------------------------- // Data class to hold problem // --------------------------------------------------------------------- class Data { public: // global settings char *version; int 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_dpd,style_ellipsoid,style_full,style_granular; int style_hybrid,style_molecular,style_peri; int natoms,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; // force fields char *pair_style,*bond_style,*angle_style,*dihedral_style,*improper_style; 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_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_start,*pair_soft_stop; 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_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; 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 *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 int iatoms,ibonds,iangles,idihedrals,iimpropers; double *mass,*shape,*dipole; double *x,*y,*z,*vx,*vy,*vz; double *omegax,*omegay,*omegaz; int *tag,*type,*mask,*image; int *molecule; double *q,*mux,*muy,*muz,*radius,*density,*vfrac,*rmass; double *s0,*x0x,*x0y,*x0z; double *quatw,*quati,*quatj,*quatk,*angmomx,*angmomy,*angmomz; 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 *fp, FILE *fp2=NULL); 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_dpd(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_granular(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_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_dpd_extra(FILE *, int); void write_atom_ellipsoid_extra(FILE *, int); void write_atom_full_extra(FILE *, int); void write_atom_granular_extra(FILE *, int); void write_atom_molecular_extra(FILE *, int); void write_atom_peri_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_dpd(FILE *, int); void write_vel_ellipsoid(FILE *, int); void write_vel_full(FILE *, int); void write_vel_granular(FILE *, int); void write_vel_molecular(FILE *, int); void write_vel_peri(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_dpd_extra(FILE *, int); void write_vel_ellipsoid_extra(FILE *, int); void write_vel_full_extra(FILE *, int); void write_vel_granular_extra(FILE *, int); void write_vel_molecular_extra(FILE *, int); void write_vel_peri_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_dpd(Data &data); void allocate_ellipsoid(Data &data); void allocate_full(Data &data); void allocate_granular(Data &data); void allocate_molecular(Data &data); void allocate_peri(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_dpd(double *, Data &, int); int atom_ellipsoid(double *, Data &, int); int atom_full(double *, Data &, int); int atom_granular(double *, Data &, int); int atom_molecular(double *, Data &, int); int atom_peri(double *, Data &, int); int read_int(FILE *fp); double read_double(FILE *fp); char *read_char(FILE *fp); // --------------------------------------------------------------------- // main program // --------------------------------------------------------------------- int main (int argc, char **argv) { // syntax error check if ((argc != 3) && (argc !=4)) { printf("Syntax: restart2data restart-file data-file (input-file)\n"); return 1; } // if restart file contains '%', file = filename with % replaced by "base" // else file = single file int multiproc; char *file,*ptr; if (ptr = strchr(argv[1],'%')) { multiproc = 1; file = new char[strlen(argv[1]) + 16]; *ptr = '\0'; sprintf(file,"%s%s%s",argv[1],"base",ptr+1); } else { multiproc = 0; file = argv[1]; } // open single restart file or base file for multiproc case printf("Reading restart file ...\n"); FILE *fp = fopen(file,"rb"); if (fp == NULL) { printf("ERROR: Cannot open restart file %s\n",file); return 1; } // read beginning of restart file Data data; header(fp,data); 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); sprintf(file,"%s%d%s",argv[1],iproc,ptr+1); fp = fopen(file,"rb"); if (fp == NULL) { printf("ERROR: Cannot open restart file %s\n",file); return 1; } } n = read_int(fp); if (n > maxbuf) { maxbuf = n; delete [] buf; buf = new double[maxbuf]; } fread(buf,sizeof(double),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 (argc == 3) { printf("Writing data file ...\n"); fp = fopen(argv[2],"w"); if (fp == NULL) { printf("ERROR: Cannot open data file %s\n",argv[2]); return 1; } data.write(fp); fclose(fp); // write out data file and input file } else { printf("Writing data file ...\n"); fp = fopen(argv[2],"w"); if (fp == NULL) { printf("ERROR: Cannot open data file %s\n",argv[2]); return 1; } printf("Writing input file ...\n"); FILE *fp2 = fopen(argv[3],"w"); if (fp2 == NULL) { printf("ERROR: Cannot open input file %s\n",argv[3]); return 1; } data.write(fp,fp2); fclose(fp); fclose(fp2); } return 0; } // --------------------------------------------------------------------- // read header of restart file // --------------------------------------------------------------------- void header(FILE *fp, Data &data) { char *version = "9 Jan 2009"; 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) { char *str = "Restart file version does not match restart2data version"; printf("WARNING %s\n",str); printf(" restart2data version = %s\n",version); } } else if (flag == UNITS) data.unit_style = read_char(fp); else if (flag == NTIMESTEP) data.ntimestep = read_int(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_dpd = data.style_ellipsoid = data.style_full = data.style_granular = data.style_hybrid = data.style_molecular = data.style_peri = 0; data.atom_style = read_char(fp); 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); set_style(substyle,data,i); } } } else if (flag == NATOMS) data.natoms = static_cast (read_double(fp)); else if (flag == NTYPES) data.ntypes = read_int(fp); else if (flag == NBONDS) data.nbonds = read_int(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_int(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_int(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_int(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,"dpd") == 0) data.style_dpd = 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,"granular") == 0) data.style_granular = flag; else if (strcmp(name,"hybrid") == 0) data.style_hybrid = flag; else if (strcmp(name,"molecular") == 0) data.style_molecular = flag; else if (strcmp(name,"peri") == 0) data.style_peri = 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); int n; 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); delete [] name; + count++; + if (count == ngroup) break; } } // --------------------------------------------------------------------- // read type arrays from restart file // --------------------------------------------------------------------- void type_arrays(FILE *fp, Data &data) { data.mass = NULL; data.shape = NULL; data.dipole = NULL; int flag; flag = read_int(fp); while (flag >= 0) { if (flag == MASS) { data.mass = new double[data.ntypes+1]; fread(&data.mass[1],sizeof(double),data.ntypes,fp); } else if (flag == SHAPE) { data.shape = new double[3*(data.ntypes+1)]; fread(&data.shape[3],sizeof(double),3*data.ntypes,fp); } else if (flag == DIPOLE) { data.dipole = new double[data.ntypes+1]; fread(&data.dipole[1],sizeof(double),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); pair(fp,data,data.pair_style,1); } else if (flag == BOND) { data.bond_style = read_char(fp); bond(fp,data); } else if (flag == ANGLE) { data.angle_style = read_char(fp); angle(fp,data); } else if (flag == DIHEDRAL) { data.dihedral_style = read_char(fp); dihedral(fp,data); } else if (flag == IMPROPER) { data.improper_style = read_char(fp); 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 int[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_dpd) allocate_dpd(data); if (data.style_ellipsoid) allocate_ellipsoid(data); if (data.style_full) allocate_full(data); if (data.style_granular) allocate_granular(data); if (data.style_molecular) allocate_molecular(data); if (data.style_peri) allocate_peri(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_dpd) m += atom_dpd(&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_granular) m += atom_granular(&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); } data.iatoms++; m = static_cast (buf[0]); return m; } // --------------------------------------------------------------------- // read one atom's info from buffer // one routine per atom style // --------------------------------------------------------------------- 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 (buf[m++]); data.type[iatoms] = static_cast (buf[m++]); data.mask[iatoms] = static_cast (buf[m++]); data.image[iatoms] = static_cast (buf[m++]); data.vx[iatoms] = buf[m++]; data.vy[iatoms] = buf[m++]; data.vz[iatoms] = buf[m++]; data.molecule[iatoms] = static_cast (buf[m++]); int n = static_cast (buf[m++]); for (int k = 0; k < n; k++) { type = static_cast (buf[m++]); atom1 = static_cast (buf[m++]); if (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 (buf[m++]); for (int k = 0; k < n; k++) { type = static_cast (buf[m++]); atom1 = static_cast (buf[m++]); atom2 = static_cast (buf[m++]); atom3 = static_cast (buf[m++]); if (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 (buf[m++]); data.type[iatoms] = static_cast (buf[m++]); data.mask[iatoms] = static_cast (buf[m++]); data.image[iatoms] = static_cast (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 (buf[m++]); data.type[iatoms] = static_cast (buf[m++]); data.mask[iatoms] = static_cast (buf[m++]); data.image[iatoms] = static_cast (buf[m++]); data.vx[iatoms] = buf[m++]; data.vy[iatoms] = buf[m++]; data.vz[iatoms] = buf[m++]; data.molecule[iatoms] = static_cast (buf[m++]); int n = static_cast (buf[m++]); for (int k = 0; k < n; k++) { type = static_cast (buf[m++]); atom1 = static_cast (buf[m++]); if (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 (buf[m++]); data.type[iatoms] = static_cast (buf[m++]); data.mask[iatoms] = static_cast (buf[m++]); data.image[iatoms] = static_cast (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 (buf[m++]); data.type[iatoms] = static_cast (buf[m++]); data.mask[iatoms] = static_cast (buf[m++]); data.image[iatoms] = static_cast (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++]; return m; } int atom_dpd(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 (buf[m++]); data.type[iatoms] = static_cast (buf[m++]); data.mask[iatoms] = static_cast (buf[m++]); data.image[iatoms] = static_cast (buf[m++]); data.vx[iatoms] = buf[m++]; data.vy[iatoms] = buf[m++]; data.vz[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 (buf[m++]); data.type[iatoms] = static_cast (buf[m++]); data.mask[iatoms] = static_cast (buf[m++]); data.image[iatoms] = static_cast (buf[m++]); data.vx[iatoms] = buf[m++]; data.vy[iatoms] = buf[m++]; data.vz[iatoms] = buf[m++]; data.quatw[iatoms] = buf[m++]; data.quati[iatoms] = buf[m++]; data.quatj[iatoms] = buf[m++]; data.quatk[iatoms] = buf[m++]; data.angmomx[iatoms] = buf[m++]; data.angmomy[iatoms] = buf[m++]; data.angmomz[iatoms] = buf[m++]; return m; } int atom_granular(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 (buf[m++]); data.type[iatoms] = static_cast (buf[m++]); data.mask[iatoms] = static_cast (buf[m++]); data.image[iatoms] = static_cast (buf[m++]); data.vx[iatoms] = buf[m++]; data.vy[iatoms] = buf[m++]; data.vz[iatoms] = buf[m++]; data.radius[iatoms] = buf[m++]; data.density[iatoms] = buf[m++]; data.omegax[iatoms] = buf[m++]; data.omegay[iatoms] = buf[m++]; data.omegaz[iatoms] = buf[m++]; 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 (buf[m++]); data.type[iatoms] = static_cast (buf[m++]); data.mask[iatoms] = static_cast (buf[m++]); data.image[iatoms] = static_cast (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 (buf[m++]); int n = static_cast (buf[m++]); for (int k = 0; k < n; k++) { type = static_cast (buf[m++]); atom1 = static_cast (buf[m++]); if (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 (buf[m++]); for (int k = 0; k < n; k++) { type = static_cast (buf[m++]); atom1 = static_cast (buf[m++]); atom2 = static_cast (buf[m++]); atom3 = static_cast (buf[m++]); if (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 (buf[m++]); for (int k = 0; k < n; k++) { type = static_cast (buf[m++]); atom1 = static_cast (buf[m++]); atom2 = static_cast (buf[m++]); atom3 = static_cast (buf[m++]); atom4 = static_cast (buf[m++]); if (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 (buf[m++]); for (int k = 0; k < n; k++) { type = static_cast (buf[m++]); atom1 = static_cast (buf[m++]); atom2 = static_cast (buf[m++]); atom3 = static_cast (buf[m++]); atom4 = static_cast (buf[m++]); if (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_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 (buf[m++]); data.type[iatoms] = static_cast (buf[m++]); data.mask[iatoms] = static_cast (buf[m++]); data.image[iatoms] = static_cast (buf[m++]); data.vx[iatoms] = buf[m++]; data.vy[iatoms] = buf[m++]; data.vz[iatoms] = buf[m++]; data.molecule[iatoms] = static_cast (buf[m++]); int n = static_cast (buf[m++]); for (int k = 0; k < n; k++) { type = static_cast (buf[m++]); atom1 = static_cast (buf[m++]); if (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 (buf[m++]); for (int k = 0; k < n; k++) { type = static_cast (buf[m++]); atom1 = static_cast (buf[m++]); atom2 = static_cast (buf[m++]); atom3 = static_cast (buf[m++]); if (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 (buf[m++]); for (int k = 0; k < n; k++) { type = static_cast (buf[m++]); atom1 = static_cast (buf[m++]); atom2 = static_cast (buf[m++]); atom3 = static_cast (buf[m++]); atom4 = static_cast (buf[m++]); if (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 (buf[m++]); for (int k = 0; k < n; k++) { type = static_cast (buf[m++]); atom1 = static_cast (buf[m++]); atom2 = static_cast (buf[m++]); atom3 = static_cast (buf[m++]); atom4 = static_cast (buf[m++]); if (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 (buf[m++]); data.type[iatoms] = static_cast (buf[m++]); data.mask[iatoms] = static_cast (buf[m++]); data.image[iatoms] = static_cast (buf[m++]); data.vx[iatoms] = buf[m++]; data.vy[iatoms] = buf[m++]; data.vz[iatoms] = buf[m++]; data.vfrac[iatoms] = buf[m++]; data.density[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; } // --------------------------------------------------------------------- // 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]; } void allocate_dpd(Data &data) {} 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.quatw = new double[data.natoms]; data.quati = new double[data.natoms]; data.quatj = new double[data.natoms]; data.quatk = new double[data.natoms]; data.angmomx = new double[data.natoms]; data.angmomy = new double[data.natoms]; data.angmomz = new double[data.natoms]; } void allocate_granular(Data &data) { data.radius = 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.density = 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]; } // --------------------------------------------------------------------- // 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,"airebo") == 0) { } else if ((strcmp(style,"buck") == 0) || (strcmp(style,"buck/coul/cut") == 0) || (strcmp(style,"buck/coul/long") == 0) || (strcmp(style,"buck/coul") == 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); } 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); } 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); } else if (strcmp(style,"buck/coul") == 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 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,"coul/cut") == 0) || (strcmp(style,"coul/debye") == 0) || (strcmp(style,"coul/long") == 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); } 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); } 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,"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,"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,"eam") == 0) { } else if (strcmp(style,"eam/opt") == 0) { } else if (strcmp(style,"eam/alloy") == 0) { } else if (strcmp(style,"eam/alloy/opt") == 0) { } else if (strcmp(style,"eam/fs") == 0) { } else if (strcmp(style,"eam/fs/opt") == 0) { } 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,"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); } else if ((strcmp(style,"lj/charmm/coul/charmm") == 0) || (strcmp(style,"lj/charmm/coul/charmm/implicit") == 0) || (strcmp(style,"lj/charmm/coul/long") == 0) || (strcmp(style,"lj/charmm/coul/long/opt") == 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") == 0) || (strcmp(style,"lj/charmm/coul/long/opt") == 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); } 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") == 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); } 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); } 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); } 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,"lj/cut/opt") == 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/tip4p") == 0) || (strcmp(style,"lj/coul") == 0)) { if ((strcmp(style,"lj/cut") == 0) || (strcmp(style,"lj/cut/opt") == 0)) { m = 0; double cut_lj_global = read_double(fp); int offset_flag = read_int(fp); int mix_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); } 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); } 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); } else if (strcmp(style,"lj/cut/coul/long/tip4p") == 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); } else if (strcmp(style,"lj/coul") == 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 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); 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,"morse") == 0) || (strcmp(style,"morse/opt") == 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,"soft") == 0) { double cut_global = read_double(fp); int mix_flag = read_int(fp); if (!flag) return; data.pair_soft_start = new double[data.ntypes+1]; data.pair_soft_stop = 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_start[i] = read_double(fp); data.pair_soft_stop[i] = read_double(fp); double cut = read_double(fp); } else { double soft_start = read_double(fp); double soft_stop = 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,"yukawa") == 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/cut") == 0) || (strcmp(style,"cg/cmm/coul/long") == 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") == 0) || (strcmp(style,"cg/cmm/coul/long") == 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") == 0) || (strcmp(style,"cg/cmm/coul/long") == 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); 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]; fread(&data.bond_class2_r0[1],sizeof(double),data.nbondtypes,fp); fread(&data.bond_class2_k2[1],sizeof(double),data.nbondtypes,fp); fread(&data.bond_class2_k3[1],sizeof(double),data.nbondtypes,fp); fread(&data.bond_class2_k4[1],sizeof(double),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]; fread(&data.bond_fene_k[1],sizeof(double),data.nbondtypes,fp); fread(&data.bond_fene_r0[1],sizeof(double),data.nbondtypes,fp); fread(&data.bond_fene_epsilon[1],sizeof(double),data.nbondtypes,fp); fread(&data.bond_fene_sigma[1],sizeof(double),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]; fread(&data.bond_feneexpand_k[1],sizeof(double),data.nbondtypes,fp); fread(&data.bond_feneexpand_r0[1],sizeof(double),data.nbondtypes,fp); fread(&data.bond_feneexpand_epsilon[1],sizeof(double),data.nbondtypes,fp); fread(&data.bond_feneexpand_sigma[1],sizeof(double),data.nbondtypes,fp); fread(&data.bond_feneexpand_shift[1],sizeof(double),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]; fread(&data.bond_harmonic_k[1],sizeof(double),data.nbondtypes,fp); fread(&data.bond_harmonic_r0[1],sizeof(double),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]; fread(&data.bond_morse_d0[1],sizeof(double),data.nbondtypes,fp); fread(&data.bond_morse_alpha[1],sizeof(double),data.nbondtypes,fp); fread(&data.bond_morse_r0[1],sizeof(double),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]; fread(&data.bond_nonlinear_epsilon[1],sizeof(double),data.nbondtypes,fp); fread(&data.bond_nonlinear_r0[1],sizeof(double),data.nbondtypes,fp); fread(&data.bond_nonlinear_lamda[1],sizeof(double),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]; fread(&data.bond_quartic_k[1],sizeof(double),data.nbondtypes,fp); fread(&data.bond_quartic_b1[1],sizeof(double),data.nbondtypes,fp); fread(&data.bond_quartic_b2[1],sizeof(double),data.nbondtypes,fp); fread(&data.bond_quartic_rc[1],sizeof(double),data.nbondtypes,fp); fread(&data.bond_quartic_u0[1],sizeof(double),data.nbondtypes,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,"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]; fread(&data.angle_charmm_k[1],sizeof(double),data.nangletypes,fp); fread(&data.angle_charmm_theta0[1],sizeof(double),data.nangletypes,fp); fread(&data.angle_charmm_k_ub[1],sizeof(double),data.nangletypes,fp); fread(&data.angle_charmm_r_ub[1],sizeof(double),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]; fread(&data.angle_class2_theta0[1],sizeof(double),data.nangletypes,fp); fread(&data.angle_class2_k2[1],sizeof(double),data.nangletypes,fp); fread(&data.angle_class2_k3[1],sizeof(double),data.nangletypes,fp); fread(&data.angle_class2_k4[1],sizeof(double),data.nangletypes,fp); fread(&data.angle_class2_bb_k[1],sizeof(double),data.nangletypes,fp); fread(&data.angle_class2_bb_r1[1],sizeof(double),data.nangletypes,fp); fread(&data.angle_class2_bb_r2[1],sizeof(double),data.nangletypes,fp); fread(&data.angle_class2_ba_k1[1],sizeof(double),data.nangletypes,fp); fread(&data.angle_class2_ba_k2[1],sizeof(double),data.nangletypes,fp); fread(&data.angle_class2_ba_r1[1],sizeof(double),data.nangletypes,fp); fread(&data.angle_class2_ba_r2[1],sizeof(double),data.nangletypes,fp); } else if (strcmp(data.angle_style,"cosine") == 0) { data.angle_cosine_k = new double[data.nangletypes+1]; fread(&data.angle_cosine_k[1],sizeof(double),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]; fread(&data.angle_cosine_squared_k[1],sizeof(double),data.nangletypes,fp); fread(&data.angle_cosine_squared_theta0[1], sizeof(double),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]; fread(&data.angle_harmonic_k[1],sizeof(double),data.nangletypes,fp); fread(&data.angle_harmonic_theta0[1],sizeof(double),data.nangletypes,fp); } else if (strcmp(data.angle_style,"cg/cmm") == 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]; fread(&data.angle_harmonic_k[1],sizeof(double),data.nangletypes,fp); fread(&data.angle_harmonic_theta0[1],sizeof(double),data.nangletypes,fp); fread(&data.angle_cg_cmm_epsilon[1],sizeof(double),data.nangletypes,fp); fread(&data.angle_cg_cmm_sigma[1],sizeof(double),data.nangletypes,fp); fread(angle_cg_cmm_rcut,sizeof(double),data.nangletypes,fp); fread(&data.angle_cg_cmm_type[1],sizeof(int),data.nangletypes,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) { 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]; fread(&data.dihedral_charmm_k[1],sizeof(double),data.ndihedraltypes,fp); fread(&data.dihedral_charmm_multiplicity[1],sizeof(int), data.ndihedraltypes,fp); fread(&data.dihedral_charmm_sign[1],sizeof(int),data.ndihedraltypes,fp); fread(&data.dihedral_charmm_weight[1],sizeof(double), data.ndihedraltypes,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]; fread(&data.dihedral_class2_k1[1],sizeof(double),data.ndihedraltypes,fp); fread(&data.dihedral_class2_k2[1],sizeof(double),data.ndihedraltypes,fp); fread(&data.dihedral_class2_k3[1],sizeof(double),data.ndihedraltypes,fp); fread(&data.dihedral_class2_phi1[1],sizeof(double),data.ndihedraltypes,fp); fread(&data.dihedral_class2_phi2[1],sizeof(double),data.ndihedraltypes,fp); fread(&data.dihedral_class2_phi3[1],sizeof(double),data.ndihedraltypes,fp); fread(&data.dihedral_class2_mbt_f1[1],sizeof(double), data.ndihedraltypes,fp); fread(&data.dihedral_class2_mbt_f2[1],sizeof(double), data.ndihedraltypes,fp); fread(&data.dihedral_class2_mbt_f3[1],sizeof(double), data.ndihedraltypes,fp); fread(&data.dihedral_class2_mbt_r0[1],sizeof(double), data.ndihedraltypes,fp); fread(&data.dihedral_class2_ebt_f1_1[1],sizeof(double), data.ndihedraltypes,fp); fread(&data.dihedral_class2_ebt_f2_1[1],sizeof(double), data.ndihedraltypes,fp); fread(&data.dihedral_class2_ebt_f3_1[1],sizeof(double), data.ndihedraltypes,fp); fread(&data.dihedral_class2_ebt_r0_1[1],sizeof(double), data.ndihedraltypes,fp); fread(&data.dihedral_class2_ebt_f1_2[1],sizeof(double), data.ndihedraltypes,fp); fread(&data.dihedral_class2_ebt_f2_2[1],sizeof(double), data.ndihedraltypes,fp); fread(&data.dihedral_class2_ebt_f3_2[1],sizeof(double), data.ndihedraltypes,fp); fread(&data.dihedral_class2_ebt_r0_2[1],sizeof(double), data.ndihedraltypes,fp); fread(&data.dihedral_class2_at_f1_1[1],sizeof(double), data.ndihedraltypes,fp); fread(&data.dihedral_class2_at_f2_1[1],sizeof(double), data.ndihedraltypes,fp); fread(&data.dihedral_class2_at_f3_1[1],sizeof(double), data.ndihedraltypes,fp); fread(&data.dihedral_class2_at_theta0_1[1],sizeof(double), data.ndihedraltypes,fp); fread(&data.dihedral_class2_at_f1_2[1],sizeof(double), data.ndihedraltypes,fp); fread(&data.dihedral_class2_at_f2_2[1],sizeof(double), data.ndihedraltypes,fp); fread(&data.dihedral_class2_at_f3_2[1],sizeof(double), data.ndihedraltypes,fp); fread(&data.dihedral_class2_at_theta0_2[1],sizeof(double), data.ndihedraltypes,fp); fread(&data.dihedral_class2_aat_k[1],sizeof(double), data.ndihedraltypes,fp); fread(&data.dihedral_class2_aat_theta0_1[1],sizeof(double), data.ndihedraltypes,fp); fread(&data.dihedral_class2_aat_theta0_2[1],sizeof(double), data.ndihedraltypes,fp); fread(&data.dihedral_class2_bb13_k[1],sizeof(double), data.ndihedraltypes,fp); fread(&data.dihedral_class2_bb13_r10[1],sizeof(double), data.ndihedraltypes,fp); fread(&data.dihedral_class2_bb13_r30[1],sizeof(double), 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]; fread(&data.dihedral_harmonic_k[1],sizeof(double),data.ndihedraltypes,fp); fread(&data.dihedral_harmonic_multiplicity[1],sizeof(int), data.ndihedraltypes,fp); fread(&data.dihedral_harmonic_sign[1],sizeof(int),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]; fread(&data.dihedral_helix_aphi[1],sizeof(double),data.ndihedraltypes,fp); fread(&data.dihedral_helix_bphi[1],sizeof(double),data.ndihedraltypes,fp); fread(&data.dihedral_helix_cphi[1],sizeof(double),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]; fread(&data.dihedral_multi_a1[1],sizeof(double),data.ndihedraltypes,fp); fread(&data.dihedral_multi_a2[1],sizeof(double),data.ndihedraltypes,fp); fread(&data.dihedral_multi_a3[1],sizeof(double),data.ndihedraltypes,fp); fread(&data.dihedral_multi_a4[1],sizeof(double),data.ndihedraltypes,fp); fread(&data.dihedral_multi_a5[1],sizeof(double),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]; fread(&data.dihedral_opls_k1[1],sizeof(double),data.ndihedraltypes,fp); fread(&data.dihedral_opls_k2[1],sizeof(double),data.ndihedraltypes,fp); fread(&data.dihedral_opls_k3[1],sizeof(double),data.ndihedraltypes,fp); fread(&data.dihedral_opls_k4[1],sizeof(double),data.ndihedraltypes,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]; fread(&data.improper_class2_k0[1],sizeof(double), data.nimpropertypes,fp); fread(&data.improper_class2_chi0[1],sizeof(double), data.nimpropertypes,fp); fread(&data.improper_class2_aa_k1[1],sizeof(double), data.nimpropertypes,fp); fread(&data.improper_class2_aa_k2[1],sizeof(double), data.nimpropertypes,fp); fread(&data.improper_class2_aa_k3[1],sizeof(double), data.nimpropertypes,fp); fread(&data.improper_class2_aa_theta0_1[1],sizeof(double), data.nimpropertypes,fp); fread(&data.improper_class2_aa_theta0_2[1],sizeof(double), data.nimpropertypes,fp); fread(&data.improper_class2_aa_theta0_3[1],sizeof(double), 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]; fread(&data.improper_cvff_k[1],sizeof(double),data.nimpropertypes,fp); fread(&data.improper_cvff_sign[1],sizeof(int),data.nimpropertypes,fp); fread(&data.improper_cvff_multiplicity[1],sizeof(int), 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]; fread(&data.improper_harmonic_k[1],sizeof(double),data.nimpropertypes,fp); fread(&data.improper_harmonic_chi[1],sizeof(double), 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() {} // --------------------------------------------------------------------- // print out stats on problem // --------------------------------------------------------------------- void Data::stats() { printf(" Restart file version = %s\n",version); printf(" Ntimestep = %d\n",ntimestep); printf(" Nprocs = %d\n",nprocs); printf(" Natoms = %d\n",natoms); printf(" Nbonds = %d\n",nbonds); printf(" Nangles = %d\n",nangles); printf(" Ndihedrals = %d\n",ndihedrals); printf(" Nimpropers = %d\n",nimpropers); printf(" Unit style = %s\n",unit_style); printf(" Atom style = %s\n",atom_style); printf(" Pair style = %s\n",pair_style); printf(" Bond style = %s\n",bond_style); printf(" Angle style = %s\n",angle_style); printf(" Dihedral style = %s\n",dihedral_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 // --------------------------------------------------------------------- void Data::write(FILE *fp, FILE *fp2) { fprintf(fp,"LAMMPS data file from restart file: timestep = %d, procs = %d\n", ntimestep,nprocs); fprintf(fp,"\n"); fprintf(fp,"%d atoms\n",natoms); if (nbonds) fprintf(fp,"%d bonds\n",nbonds); if (nangles) fprintf(fp,"%d angles\n",nangles); if (ndihedrals) fprintf(fp,"%d dihedrals\n",ndihedrals); if (nimpropers) fprintf(fp,"%d impropers\n",nimpropers); 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 = %d, 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 %g %g %g %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 either data file or input file 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"); } else { fprintf(fp,"\nMasses\n\n"); for (int i = 1; i <= ntypes; i++) fprintf(fp,"%d %g\n",i,mass[i]); } } // shape and dipole to data file // convert shape from radius to diameter if (shape) { fprintf(fp,"\nShapes\n\n"); for (int i = 1; i <= ntypes; i++) fprintf(fp,"%d %g %g %g\n",i, 2.0*shape[3*i+0],2.0*shape[3*i+1],2.0*shape[3*i+2]); } if (dipole) { fprintf(fp,"\nDipoles\n\n"); for (int i = 1; i <= ntypes; i++) fprintf(fp,"%d %g\n",i,dipole[i]); } // pair coeffs to data file if (pair_style && fp2 == NULL) { if ((strcmp(pair_style,"none") != 0) && (strcmp(pair_style,"airebo") != 0) && (strcmp(pair_style,"coul/cut") != 0) && (strcmp(pair_style,"coul/debye") != 0) && (strcmp(pair_style,"coul/long") != 0) && (strcmp(pair_style,"eam") != 0) && (strcmp(pair_style,"eam/opt") != 0) && (strcmp(pair_style,"eam/alloy") != 0) && (strcmp(pair_style,"eam/alloy/opt") != 0) && (strcmp(pair_style,"eam/fs") != 0) && (strcmp(pair_style,"eam/fs/opt") != 0) && (strcmp(pair_style,"meam") != 0) && (strcmp(pair_style,"gran/history") != 0) && (strcmp(pair_style,"gran/no_history") != 0) && (strcmp(pair_style,"gran/hertzian") != 0) && (strcmp(pair_style,"sw") != 0) && (strcmp(pair_style,"table") != 0) && (strcmp(pair_style,"tersoff") != 0) && (strcmp(pair_style,"hybrid") != 0) && (strcmp(pair_style,"hybrid/overlay") != 0)) fprintf(fp,"\nPair Coeffs\n\n"); 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) { 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,"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") == 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") == 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,"lj/cut/opt") == 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/tip4p") == 0) | (strcmp(pair_style,"lj/coul") == 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) || (strcmp(pair_style,"morse/opt") == 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 %g\n",i, pair_soft_start[i],pair_soft_stop[i]); } else if (strcmp(pair_style,"yukawa") == 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)) { printf("ERROR: Cannot write pair_style %s to data file\n", pair_style); exit(1); } } // pair coeffs to input file // only supported styles = cg/cmm if (pair_style && fp2) { if ((strcmp(pair_style,"cg/cmm") == 0) || (strcmp(pair_style,"cg/cmm/coul/cut") == 0) || (strcmp(pair_style,"cg/cmm/coul/long") == 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 (bond_style && fp2 == NULL) { if ((strcmp(bond_style,"none") != 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,"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 (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 (angle_style && fp2 == NULL) { double PI = 3.1415926; // convert back to degrees if ((strcmp(angle_style,"none") != 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,"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,"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) { 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 (angle_style && fp2) { double PI = 3.1415926; // convert back to degrees 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) { 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 (dihedral_style) { double PI = 3.1415926; // convert back to degrees if ((strcmp(dihedral_style,"none") != 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,"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 (improper_style) { double PI = 3.1415926; // convert back to degrees 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 (int i = 0; i < natoms; i++) { ix = (image[i] & 1023) - 512; iy = (image[i] >> 10 & 1023) - 512; iz = (image[i] >> 20) - 512; 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_dpd) write_atom_dpd(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_granular) write_atom_granular(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); 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_dpd) write_atom_dpd_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_granular) write_atom_granular_extra(fp,i); if (k == style_molecular) write_atom_molecular_extra(fp,i); if (k == style_peri) write_atom_peri_extra(fp,i); } fprintf(fp," %d %d %d\n",ix,iy,iz); } } } if (natoms) { fprintf(fp,"\nVelocities\n\n"); for (int 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_dpd) write_vel_dpd(fp,i); if (style_ellipsoid) write_vel_ellipsoid(fp,i); if (style_full) write_vel_full(fp,i); if (style_granular) write_vel_granular(fp,i); if (style_molecular) write_vel_molecular(fp,i); if (style_peri) write_vel_peri(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_dpd) write_vel_dpd_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_granular) write_vel_granular_extra(fp,i); if (k == style_molecular) write_vel_molecular_extra(fp,i); if (k == style_peri) write_vel_peri_extra(fp,i); } fprintf(fp,"\n"); } } if (nbonds) { fprintf(fp,"\nBonds\n\n"); for (int i = 0; i < nbonds; i++) fprintf(fp,"%d %d %d %d\n", i+1,bond_type[i],bond_atom1[i],bond_atom2[i]); } if (nangles) { fprintf(fp,"\nAngles\n\n"); for (int i = 0; i < nangles; i++) fprintf(fp,"%d %d %d %d %d\n", i+1,angle_type[i],angle_atom1[i],angle_atom2[i],angle_atom3[i]); } if (ndihedrals) { fprintf(fp,"\nDihedrals\n\n"); for (int i = 0; i < ndihedrals; i++) fprintf(fp,"%d %d %d %d %d %d\n", i+1,dihedral_type[i],dihedral_atom1[i],dihedral_atom2[i], dihedral_atom3[i],dihedral_atom4[i]); } if (nimpropers) { fprintf(fp,"\nImpropers\n\n"); for (int i = 0; i < nimpropers; i++) fprintf(fp,"%d %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],mux[i],muy[i],muz[i],ix,iy,iz); } void Data::write_atom_dpd(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_ellipsoid(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],x[i],y[i],z[i], quatw[i],quati[i],quatj[i],quatk[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_granular(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_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 %-1.16e %d %d %d", tag[i],type[i],vfrac[i],density[i],rmass[i],x[i],y[i],z[i],ix,iy,iz); } // --------------------------------------------------------------------- // 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],mux[i],muy[i],muz[i]); } void Data::write_atom_dpd_extra(FILE *fp, int i) {} void Data::write_atom_ellipsoid_extra(FILE *fp, int i) { fprintf(fp," %-1.16e %-1.16e %-1.16e %-1.16e",quatw[i],quati[i],quatj[i],quatk[i]); } void Data::write_atom_full_extra(FILE *fp, int i) { fprintf(fp," %d %-1.16e",molecule[i],q[i]); } void Data::write_atom_granular_extra(FILE *fp, int i) { fprintf(fp," %-1.16e %-1.16e",2.0*radius[i],density[i]); } 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 %-1.16e",vfrac[i],density[i],rmass[i]); } // --------------------------------------------------------------------- // 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_dpd(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_granular(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_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]); } // --------------------------------------------------------------------- // 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_dpd_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_granular_extra(FILE *fp, int i) { fprintf(fp," %-1.16e %-1.16e %-1.16e",omegax[i],omegay[i],omegaz[i]); } void Data::write_vel_molecular_extra(FILE *fp, int i) {} void Data::write_vel_peri_extra(FILE *fp, int i) {} // --------------------------------------------------------------------- // binary reads from restart file // --------------------------------------------------------------------- int read_int(FILE *fp) { int value; fread(&value,sizeof(int),1,fp); return value; } double read_double(FILE *fp) { double value; fread(&value,sizeof(double),1,fp); return value; } char *read_char(FILE *fp) { int n; fread(&n,sizeof(int),1,fp); if (n == 0) return NULL; char *value = new char[n]; fread(value,sizeof(char),n,fp); return value; }