forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7789 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
96a049ee43
commit
9add1067ad
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@ -67,6 +67,8 @@ enum{PAIR,BOND,ANGLE,DIHEDRAL,IMPROPER};
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static const char * const cg_type_list[] =
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{"none", "lj9_6", "lj12_4", "lj12_6"};
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int swapflag;
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// ---------------------------------------------------------------------
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// Data class to hold problem
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// ---------------------------------------------------------------------
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@ -341,11 +343,15 @@ int atom_wavepacket(double *, Data &, int);
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void strip_suffix(char *);
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void nread_int(int *buf, int n, FILE *fp);
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void nread_double(double *buf, int n, FILE *fp);
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int read_int(FILE *fp);
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double read_double(FILE *fp);
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char *read_char(FILE *fp);
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bigint read_bigint(FILE *fp);
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int autodetect(FILE **, char *);
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static void helpmsg(int exitval)
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{
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printf("Syntax: restart2data (switch1 switch2 ...) "
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@ -423,6 +429,10 @@ int main (int narg, char **arg)
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}
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}
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// auto-detect whether byte swapping needs to be done as file is read
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swapflag = autodetect(&fp,restartfile);
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// read beginning of restart file
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Data data;
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@ -468,7 +478,7 @@ int main (int narg, char **arg)
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buf = new double[maxbuf];
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}
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fread(buf,sizeof(double),n,fp);
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nread_double(buf,n,fp);
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m = 0;
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while (m < n) m += atom(&buf[m],data);
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@ -698,7 +708,7 @@ void type_arrays(FILE *fp, Data &data)
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if (flag == MASS) {
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data.mass = new double[data.ntypes+1];
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fread(&data.mass[1],sizeof(double),data.ntypes,fp);
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nread_double(&data.mass[1],data.ntypes,fp);
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} else {
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printf("ERROR: Invalid flag in type arrays section of restart file %d\n",
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flag);
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@ -2563,10 +2573,10 @@ void bond(FILE *fp, Data &data)
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data.bond_class2_k2 = new double[data.nbondtypes+1];
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data.bond_class2_k3 = new double[data.nbondtypes+1];
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data.bond_class2_k4 = new double[data.nbondtypes+1];
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fread(&data.bond_class2_r0[1],sizeof(double),data.nbondtypes,fp);
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fread(&data.bond_class2_k2[1],sizeof(double),data.nbondtypes,fp);
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fread(&data.bond_class2_k3[1],sizeof(double),data.nbondtypes,fp);
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fread(&data.bond_class2_k4[1],sizeof(double),data.nbondtypes,fp);
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nread_double(&data.bond_class2_r0[1],data.nbondtypes,fp);
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nread_double(&data.bond_class2_k2[1],data.nbondtypes,fp);
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nread_double(&data.bond_class2_k3[1],data.nbondtypes,fp);
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nread_double(&data.bond_class2_k4[1],data.nbondtypes,fp);
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} else if (strcmp(data.bond_style,"fene") == 0) {
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@ -2574,10 +2584,10 @@ void bond(FILE *fp, Data &data)
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data.bond_fene_r0 = new double[data.nbondtypes+1];
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data.bond_fene_epsilon = new double[data.nbondtypes+1];
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data.bond_fene_sigma = new double[data.nbondtypes+1];
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fread(&data.bond_fene_k[1],sizeof(double),data.nbondtypes,fp);
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fread(&data.bond_fene_r0[1],sizeof(double),data.nbondtypes,fp);
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fread(&data.bond_fene_epsilon[1],sizeof(double),data.nbondtypes,fp);
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fread(&data.bond_fene_sigma[1],sizeof(double),data.nbondtypes,fp);
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nread_double(&data.bond_fene_k[1],data.nbondtypes,fp);
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nread_double(&data.bond_fene_r0[1],data.nbondtypes,fp);
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nread_double(&data.bond_fene_epsilon[1],data.nbondtypes,fp);
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nread_double(&data.bond_fene_sigma[1],data.nbondtypes,fp);
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} else if (strcmp(data.bond_style,"fene/expand") == 0) {
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@ -2586,55 +2596,54 @@ void bond(FILE *fp, Data &data)
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data.bond_feneexpand_epsilon = new double[data.nbondtypes+1];
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data.bond_feneexpand_sigma = new double[data.nbondtypes+1];
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data.bond_feneexpand_shift = new double[data.nbondtypes+1];
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fread(&data.bond_feneexpand_k[1],sizeof(double),data.nbondtypes,fp);
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fread(&data.bond_feneexpand_r0[1],sizeof(double),data.nbondtypes,fp);
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fread(&data.bond_feneexpand_epsilon[1],sizeof(double),data.nbondtypes,fp);
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fread(&data.bond_feneexpand_sigma[1],sizeof(double),data.nbondtypes,fp);
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fread(&data.bond_feneexpand_shift[1],sizeof(double),data.nbondtypes,fp);
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nread_double(&data.bond_feneexpand_k[1],data.nbondtypes,fp);
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nread_double(&data.bond_feneexpand_r0[1],data.nbondtypes,fp);
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nread_double(&data.bond_feneexpand_epsilon[1],data.nbondtypes,fp);
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nread_double(&data.bond_feneexpand_sigma[1],data.nbondtypes,fp);
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nread_double(&data.bond_feneexpand_shift[1],data.nbondtypes,fp);
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} else if (strcmp(data.bond_style,"harmonic") == 0) {
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data.bond_harmonic_k = new double[data.nbondtypes+1];
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data.bond_harmonic_r0 = new double[data.nbondtypes+1];
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fread(&data.bond_harmonic_k[1],sizeof(double),data.nbondtypes,fp);
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fread(&data.bond_harmonic_r0[1],sizeof(double),data.nbondtypes,fp);
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nread_double(&data.bond_harmonic_k[1],data.nbondtypes,fp);
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nread_double(&data.bond_harmonic_r0[1],data.nbondtypes,fp);
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} else if (strcmp(data.bond_style,"harmonicshift") == 0) {
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data.bond_harmonicshift_umin = new double[data.nbondtypes+1];
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data.bond_harmonicshift_r0 = new double[data.nbondtypes+1];
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data.bond_harmonicshift_rc = new double[data.nbondtypes+1];
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fread(&data.bond_harmonicshift_umin[1],sizeof(double),data.nbondtypes,fp);
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fread(&data.bond_harmonicshift_r0[1],sizeof(double),data.nbondtypes,fp);
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fread(&data.bond_harmonicshift_rc[1],sizeof(double),data.nbondtypes,fp);
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nread_double(&data.bond_harmonicshift_umin[1],data.nbondtypes,fp);
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nread_double(&data.bond_harmonicshift_r0[1],data.nbondtypes,fp);
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nread_double(&data.bond_harmonicshift_rc[1],data.nbondtypes,fp);
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} else if (strcmp(data.bond_style,"harmonicshiftcut") == 0) {
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data.bond_harmonicshiftcut_umin = new double[data.nbondtypes+1];
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data.bond_harmonicshiftcut_r0 = new double[data.nbondtypes+1];
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data.bond_harmonicshiftcut_rc = new double[data.nbondtypes+1];
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fread(&data.bond_harmonicshiftcut_umin[1],sizeof(double),
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data.nbondtypes,fp);
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fread(&data.bond_harmonicshiftcut_r0[1],sizeof(double),data.nbondtypes,fp);
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fread(&data.bond_harmonicshiftcut_rc[1],sizeof(double),data.nbondtypes,fp);
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nread_double(&data.bond_harmonicshiftcut_umin[1],data.nbondtypes,fp);
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nread_double(&data.bond_harmonicshiftcut_r0[1],data.nbondtypes,fp);
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nread_double(&data.bond_harmonicshiftcut_rc[1],data.nbondtypes,fp);
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} else if (strcmp(data.bond_style,"morse") == 0) {
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data.bond_morse_d0 = new double[data.nbondtypes+1];
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data.bond_morse_alpha = new double[data.nbondtypes+1];
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data.bond_morse_r0 = new double[data.nbondtypes+1];
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fread(&data.bond_morse_d0[1],sizeof(double),data.nbondtypes,fp);
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fread(&data.bond_morse_alpha[1],sizeof(double),data.nbondtypes,fp);
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fread(&data.bond_morse_r0[1],sizeof(double),data.nbondtypes,fp);
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nread_double(&data.bond_morse_d0[1],data.nbondtypes,fp);
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nread_double(&data.bond_morse_alpha[1],data.nbondtypes,fp);
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nread_double(&data.bond_morse_r0[1],data.nbondtypes,fp);
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} else if (strcmp(data.bond_style,"nonlinear") == 0) {
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data.bond_nonlinear_epsilon = new double[data.nbondtypes+1];
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data.bond_nonlinear_r0 = new double[data.nbondtypes+1];
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data.bond_nonlinear_lamda = new double[data.nbondtypes+1];
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fread(&data.bond_nonlinear_epsilon[1],sizeof(double),data.nbondtypes,fp);
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fread(&data.bond_nonlinear_r0[1],sizeof(double),data.nbondtypes,fp);
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fread(&data.bond_nonlinear_lamda[1],sizeof(double),data.nbondtypes,fp);
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nread_double(&data.bond_nonlinear_epsilon[1],data.nbondtypes,fp);
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nread_double(&data.bond_nonlinear_r0[1],data.nbondtypes,fp);
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nread_double(&data.bond_nonlinear_lamda[1],data.nbondtypes,fp);
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} else if (strcmp(data.bond_style,"quartic") == 0) {
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@ -2643,11 +2652,11 @@ void bond(FILE *fp, Data &data)
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data.bond_quartic_b2 = new double[data.nbondtypes+1];
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data.bond_quartic_rc = new double[data.nbondtypes+1];
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data.bond_quartic_u0 = new double[data.nbondtypes+1];
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fread(&data.bond_quartic_k[1],sizeof(double),data.nbondtypes,fp);
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fread(&data.bond_quartic_b1[1],sizeof(double),data.nbondtypes,fp);
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fread(&data.bond_quartic_b2[1],sizeof(double),data.nbondtypes,fp);
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fread(&data.bond_quartic_rc[1],sizeof(double),data.nbondtypes,fp);
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fread(&data.bond_quartic_u0[1],sizeof(double),data.nbondtypes,fp);
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nread_double(&data.bond_quartic_k[1],data.nbondtypes,fp);
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nread_double(&data.bond_quartic_b1[1],data.nbondtypes,fp);
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nread_double(&data.bond_quartic_b2[1],data.nbondtypes,fp);
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nread_double(&data.bond_quartic_rc[1],data.nbondtypes,fp);
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nread_double(&data.bond_quartic_u0[1],data.nbondtypes,fp);
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} else if (strcmp(data.bond_style,"table") == 0) {
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@ -2682,9 +2691,9 @@ void angle(FILE *fp, Data &data)
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data.angle_harmonic_theta0 = new double[data.nangletypes+1];
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data.angle_cg_cmm_epsilon = new double[data.nangletypes+1];
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fread(&data.angle_harmonic_k[1],sizeof(double),data.nangletypes,fp);
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fread(&data.angle_harmonic_theta0[1],sizeof(double),data.nangletypes,fp);
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fread(&data.angle_cg_cmm_epsilon[1],sizeof(double),data.nangletypes,fp);
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nread_double(&data.angle_harmonic_k[1],data.nangletypes,fp);
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nread_double(&data.angle_harmonic_theta0[1],data.nangletypes,fp);
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nread_double(&data.angle_cg_cmm_epsilon[1],data.nangletypes,fp);
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} else if (strcmp(data.angle_style,"cg/cmm/old") == 0) {
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@ -2695,12 +2704,12 @@ void angle(FILE *fp, Data &data)
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double *angle_cg_cmm_rcut = new double[data.nangletypes+1];
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data.angle_cg_cmm_type = new int[data.nangletypes+1];
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fread(&data.angle_harmonic_k[1],sizeof(double),data.nangletypes,fp);
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fread(&data.angle_harmonic_theta0[1],sizeof(double),data.nangletypes,fp);
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fread(&data.angle_cg_cmm_epsilon[1],sizeof(double),data.nangletypes,fp);
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fread(&data.angle_cg_cmm_sigma[1],sizeof(double),data.nangletypes,fp);
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fread(angle_cg_cmm_rcut,sizeof(double),data.nangletypes,fp);
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fread(&data.angle_cg_cmm_type[1],sizeof(int),data.nangletypes,fp);
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nread_double(&data.angle_harmonic_k[1],data.nangletypes,fp);
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nread_double(&data.angle_harmonic_theta0[1],data.nangletypes,fp);
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nread_double(&data.angle_cg_cmm_epsilon[1],data.nangletypes,fp);
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nread_double(&data.angle_cg_cmm_sigma[1],data.nangletypes,fp);
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nread_double(angle_cg_cmm_rcut,data.nangletypes,fp);
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nread_int(&data.angle_cg_cmm_type[1],data.nangletypes,fp);
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} else if (strcmp(data.angle_style,"charmm") == 0) {
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@ -2708,10 +2717,11 @@ void angle(FILE *fp, Data &data)
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data.angle_charmm_theta0 = new double[data.nangletypes+1];
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data.angle_charmm_k_ub = new double[data.nangletypes+1];
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data.angle_charmm_r_ub = new double[data.nangletypes+1];
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fread(&data.angle_charmm_k[1],sizeof(double),data.nangletypes,fp);
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fread(&data.angle_charmm_theta0[1],sizeof(double),data.nangletypes,fp);
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fread(&data.angle_charmm_k_ub[1],sizeof(double),data.nangletypes,fp);
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fread(&data.angle_charmm_r_ub[1],sizeof(double),data.nangletypes,fp);
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nread_double(&data.angle_charmm_k[1],data.nangletypes,fp);
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nread_double(&data.angle_charmm_theta0[1],data.nangletypes,fp);
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nread_double(&data.angle_charmm_k_ub[1],data.nangletypes,fp);
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nread_double(&data.angle_charmm_r_ub[1],data.nangletypes,fp);
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} else if (strcmp(data.angle_style,"class2") == 0) {
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@ -2729,75 +2739,70 @@ void angle(FILE *fp, Data &data)
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data.angle_class2_ba_r1 = new double[data.nangletypes+1];
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data.angle_class2_ba_r2 = new double[data.nangletypes+1];
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fread(&data.angle_class2_theta0[1],sizeof(double),data.nangletypes,fp);
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fread(&data.angle_class2_k2[1],sizeof(double),data.nangletypes,fp);
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fread(&data.angle_class2_k3[1],sizeof(double),data.nangletypes,fp);
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fread(&data.angle_class2_k4[1],sizeof(double),data.nangletypes,fp);
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nread_double(&data.angle_class2_theta0[1],data.nangletypes,fp);
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nread_double(&data.angle_class2_k2[1],data.nangletypes,fp);
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nread_double(&data.angle_class2_k3[1],data.nangletypes,fp);
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nread_double(&data.angle_class2_k4[1],data.nangletypes,fp);
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fread(&data.angle_class2_bb_k[1],sizeof(double),data.nangletypes,fp);
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fread(&data.angle_class2_bb_r1[1],sizeof(double),data.nangletypes,fp);
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fread(&data.angle_class2_bb_r2[1],sizeof(double),data.nangletypes,fp);
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nread_double(&data.angle_class2_bb_k[1],data.nangletypes,fp);
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nread_double(&data.angle_class2_bb_r1[1],data.nangletypes,fp);
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nread_double(&data.angle_class2_bb_r2[1],data.nangletypes,fp);
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fread(&data.angle_class2_ba_k1[1],sizeof(double),data.nangletypes,fp);
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fread(&data.angle_class2_ba_k2[1],sizeof(double),data.nangletypes,fp);
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fread(&data.angle_class2_ba_r1[1],sizeof(double),data.nangletypes,fp);
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fread(&data.angle_class2_ba_r2[1],sizeof(double),data.nangletypes,fp);
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nread_double(&data.angle_class2_ba_k1[1],data.nangletypes,fp);
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nread_double(&data.angle_class2_ba_k2[1],data.nangletypes,fp);
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nread_double(&data.angle_class2_ba_r1[1],data.nangletypes,fp);
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nread_double(&data.angle_class2_ba_r2[1],data.nangletypes,fp);
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} else if (strcmp(data.angle_style,"cosineshift") == 0) {
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data.angle_cosineshift_umin = new double[data.nangletypes+1];
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fread(&data.angle_cosineshift_umin[1],sizeof(double),data.nangletypes,fp);
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nread_double(&data.angle_cosineshift_umin[1],data.nangletypes,fp);
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data.angle_cosineshift_cost = new double[data.nangletypes+1];
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fread(&data.angle_cosineshift_cost[1],sizeof(double),data.nangletypes,fp);
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nread_double(&data.angle_cosineshift_cost[1],data.nangletypes,fp);
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data.angle_cosineshift_sint = new double[data.nangletypes+1];
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fread(&data.angle_cosineshift_sint[1],sizeof(double),data.nangletypes,fp);
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nread_double(&data.angle_cosineshift_sint[1],data.nangletypes,fp);
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data.angle_cosineshift_theta0 = new double[data.nangletypes+1];
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fread(&data.angle_cosineshift_theta0[1],sizeof(double),data.nangletypes,fp);
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nread_double(&data.angle_cosineshift_theta0[1],data.nangletypes,fp);
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} else if (strcmp(data.angle_style,"cosineshiftexp") == 0) {
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data.angle_cosineshiftexp_umin = new double[data.nangletypes+1];
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fread(&data.angle_cosineshiftexp_umin[1],sizeof(double),
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data.nangletypes,fp);
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nread_double(&data.angle_cosineshiftexp_umin[1],data.nangletypes,fp);
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data.angle_cosineshiftexp_a = new double[data.nangletypes+1];
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fread(&data.angle_cosineshiftexp_a[1],sizeof(double),data.nangletypes,fp);
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nread_double(&data.angle_cosineshiftexp_a[1],data.nangletypes,fp);
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data.angle_cosineshiftexp_cost = new double[data.nangletypes+1];
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fread(&data.angle_cosineshiftexp_cost[1],sizeof(double),
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data.nangletypes,fp);
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nread_double(&data.angle_cosineshiftexp_cost[1],data.nangletypes,fp);
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data.angle_cosineshiftexp_sint = new double[data.nangletypes+1];
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fread(&data.angle_cosineshiftexp_sint[1],sizeof(double),
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data.nangletypes,fp);
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nread_double(&data.angle_cosineshiftexp_sint[1],data.nangletypes,fp);
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data.angle_cosineshiftexp_theta0 = new double[data.nangletypes+1];
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fread(&data.angle_cosineshiftexp_theta0[1],sizeof(double),
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data.nangletypes,fp);
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nread_double(&data.angle_cosineshiftexp_theta0[1],data.nangletypes,fp);
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} else if (strcmp(data.angle_style,"cosine") == 0) {
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data.angle_cosine_k = new double[data.nangletypes+1];
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fread(&data.angle_cosine_k[1],sizeof(double),data.nangletypes,fp);
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nread_double(&data.angle_cosine_k[1],data.nangletypes,fp);
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|
||||
} 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);
|
||||
nread_double(&data.angle_cosine_squared_k[1],data.nangletypes,fp);
|
||||
nread_double(&data.angle_cosine_squared_theta0[1],data.nangletypes,fp);
|
||||
|
||||
} else if (strcmp(data.angle_style,"dipole") == 0) {
|
||||
|
||||
data.angle_harmonic_k = new double[data.nangletypes+1];
|
||||
data.angle_harmonic_theta0 = new double[data.nangletypes+1];
|
||||
fread(&data.angle_harmonic_k[1],sizeof(double),data.nangletypes,fp);
|
||||
fread(&data.angle_harmonic_theta0[1],sizeof(double),data.nangletypes,fp);
|
||||
nread_double(&data.angle_harmonic_k[1],data.nangletypes,fp);
|
||||
nread_double(&data.angle_harmonic_theta0[1],data.nangletypes,fp);
|
||||
|
||||
} else if (strcmp(data.angle_style,"harmonic") == 0) {
|
||||
|
||||
data.angle_harmonic_k = new double[data.nangletypes+1];
|
||||
data.angle_harmonic_theta0 = new double[data.nangletypes+1];
|
||||
fread(&data.angle_harmonic_k[1],sizeof(double),data.nangletypes,fp);
|
||||
fread(&data.angle_harmonic_theta0[1],sizeof(double),data.nangletypes,fp);
|
||||
nread_double(&data.angle_harmonic_k[1],data.nangletypes,fp);
|
||||
nread_double(&data.angle_harmonic_theta0[1],data.nangletypes,fp);
|
||||
|
||||
} else if (strcmp(data.angle_style,"table") == 0) {
|
||||
|
||||
|
|
@ -2831,12 +2836,10 @@ void dihedral(FILE *fp, Data &data)
|
|||
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);
|
||||
nread_double(&data.dihedral_charmm_k[1],data.ndihedraltypes,fp);
|
||||
nread_int(&data.dihedral_charmm_multiplicity[1],data.ndihedraltypes,fp);
|
||||
nread_int(&data.dihedral_charmm_sign[1],data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_charmm_weight[1],data.ndihedraltypes,fp);
|
||||
|
||||
} else if (strcmp(data.dihedral_style,"class2") == 0) {
|
||||
|
||||
|
|
@ -2880,90 +2883,63 @@ void dihedral(FILE *fp, Data &data)
|
|||
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);
|
||||
nread_double(&data.dihedral_class2_k1[1],data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_class2_k2[1],data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_class2_k3[1],data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_class2_phi1[1],data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_class2_phi2[1],data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_class2_phi3[1],data.ndihedraltypes,fp);
|
||||
|
||||
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);
|
||||
nread_double(&data.dihedral_class2_mbt_f1[1],data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_class2_mbt_f2[1],data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_class2_mbt_f3[1],data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_class2_mbt_r0[1],data.ndihedraltypes,fp);
|
||||
|
||||
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);
|
||||
nread_double(&data.dihedral_class2_ebt_f1_1[1],data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_class2_ebt_f2_1[1],data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_class2_ebt_f3_1[1],data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_class2_ebt_r0_1[1],data.ndihedraltypes,fp);
|
||||
|
||||
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);
|
||||
nread_double(&data.dihedral_class2_ebt_f1_2[1],data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_class2_ebt_f2_2[1],data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_class2_ebt_f3_2[1],data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_class2_ebt_r0_2[1],data.ndihedraltypes,fp);
|
||||
|
||||
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);
|
||||
nread_double(&data.dihedral_class2_at_f1_1[1],data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_class2_at_f2_1[1],data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_class2_at_f3_1[1],data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_class2_at_theta0_1[1],data.ndihedraltypes,fp);
|
||||
|
||||
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);
|
||||
nread_double(&data.dihedral_class2_at_f1_2[1],data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_class2_at_f2_2[1],data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_class2_at_f3_2[1],data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_class2_at_theta0_2[1],data.ndihedraltypes,fp);
|
||||
|
||||
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);
|
||||
nread_double(&data.dihedral_class2_aat_k[1],data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_class2_aat_theta0_1[1],data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_class2_aat_theta0_2[1],data.ndihedraltypes,fp);
|
||||
|
||||
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);
|
||||
nread_double(&data.dihedral_class2_bb13_k[1],data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_class2_bb13_r10[1],data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_class2_bb13_r30[1],data.ndihedraltypes,fp);
|
||||
|
||||
} else if (strcmp(data.dihedral_style,"harmonic") == 0) {
|
||||
|
||||
data.dihedral_harmonic_k = new double[data.ndihedraltypes+1];
|
||||
data.dihedral_harmonic_multiplicity = new int[data.ndihedraltypes+1];
|
||||
data.dihedral_harmonic_sign = new int[data.ndihedraltypes+1];
|
||||
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);
|
||||
nread_double(&data.dihedral_harmonic_k[1],data.ndihedraltypes,fp);
|
||||
nread_int(&data.dihedral_harmonic_multiplicity[1],data.ndihedraltypes,fp);
|
||||
nread_int(&data.dihedral_harmonic_sign[1],data.ndihedraltypes,fp);
|
||||
|
||||
} else if (strcmp(data.dihedral_style,"helix") == 0) {
|
||||
|
||||
data.dihedral_helix_aphi = new double[data.ndihedraltypes+1];
|
||||
data.dihedral_helix_bphi = new double[data.ndihedraltypes+1];
|
||||
data.dihedral_helix_cphi = new double[data.ndihedraltypes+1];
|
||||
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);
|
||||
nread_double(&data.dihedral_helix_aphi[1],data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_helix_bphi[1],data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_helix_cphi[1],data.ndihedraltypes,fp);
|
||||
|
||||
} else if (strcmp(data.dihedral_style,"multi/harmonic") == 0) {
|
||||
|
||||
|
|
@ -2972,11 +2948,11 @@ void dihedral(FILE *fp, Data &data)
|
|||
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);
|
||||
nread_double(&data.dihedral_multi_a1[1],data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_multi_a2[1],data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_multi_a3[1],data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_multi_a4[1],data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_multi_a5[1],data.ndihedraltypes,fp);
|
||||
|
||||
} else if (strcmp(data.dihedral_style,"opls") == 0) {
|
||||
|
||||
|
|
@ -2984,28 +2960,23 @@ void dihedral(FILE *fp, Data &data)
|
|||
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);
|
||||
nread_double(&data.dihedral_opls_k1[1],data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_opls_k2[1],data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_opls_k3[1],data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_opls_k4[1],data.ndihedraltypes,fp);
|
||||
|
||||
} else if (strcmp(data.dihedral_style,"cosineshiftexp") == 0) {
|
||||
|
||||
data.dihedral_cosineshiftexp_umin = new double[data.ndihedraltypes+1];
|
||||
fread(&data.dihedral_cosineshiftexp_umin[1],sizeof(double),
|
||||
data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_cosineshiftexp_umin[1],data.ndihedraltypes,fp);
|
||||
data.dihedral_cosineshiftexp_a = new double[data.ndihedraltypes+1];
|
||||
fread(&data.dihedral_cosineshiftexp_a[1],sizeof(double),
|
||||
data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_cosineshiftexp_a[1],data.ndihedraltypes,fp);
|
||||
data.dihedral_cosineshiftexp_cost = new double[data.ndihedraltypes+1];
|
||||
fread(&data.dihedral_cosineshiftexp_cost[1],sizeof(double),
|
||||
data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_cosineshiftexp_cost[1],data.ndihedraltypes,fp);
|
||||
data.dihedral_cosineshiftexp_sint = new double[data.ndihedraltypes+1];
|
||||
fread(&data.dihedral_cosineshiftexp_sint[1],sizeof(double),
|
||||
data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_cosineshiftexp_sint[1],data.ndihedraltypes,fp);
|
||||
data.dihedral_cosineshiftexp_theta = new double[data.ndihedraltypes+1];
|
||||
fread(&data.dihedral_cosineshiftexp_theta[1],sizeof(double),
|
||||
data.ndihedraltypes,fp);
|
||||
nread_double(&data.dihedral_cosineshiftexp_theta[1],data.ndihedraltypes,fp);
|
||||
|
||||
} else if (strcmp(data.dihedral_style,"table") == 0) {
|
||||
|
||||
|
|
@ -3045,41 +3016,31 @@ void improper(FILE *fp, Data &data)
|
|||
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);
|
||||
nread_double(&data.improper_class2_k0[1],data.nimpropertypes,fp);
|
||||
nread_double(&data.improper_class2_chi0[1],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);
|
||||
nread_double(&data.improper_class2_aa_k1[1],data.nimpropertypes,fp);
|
||||
nread_double(&data.improper_class2_aa_k2[1],data.nimpropertypes,fp);
|
||||
nread_double(&data.improper_class2_aa_k3[1],data.nimpropertypes,fp);
|
||||
nread_double(&data.improper_class2_aa_theta0_1[1],data.nimpropertypes,fp);
|
||||
nread_double(&data.improper_class2_aa_theta0_2[1],data.nimpropertypes,fp);
|
||||
nread_double(&data.improper_class2_aa_theta0_3[1],data.nimpropertypes,fp);
|
||||
|
||||
} else if (strcmp(data.improper_style,"cvff") == 0) {
|
||||
|
||||
data.improper_cvff_k = new double[data.nimpropertypes+1];
|
||||
data.improper_cvff_sign = new int[data.nimpropertypes+1];
|
||||
data.improper_cvff_multiplicity = new int[data.nimpropertypes+1];
|
||||
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);
|
||||
nread_double(&data.improper_cvff_k[1],data.nimpropertypes,fp);
|
||||
nread_int(&data.improper_cvff_sign[1],data.nimpropertypes,fp);
|
||||
nread_int(&data.improper_cvff_multiplicity[1],data.nimpropertypes,fp);
|
||||
|
||||
} else if (strcmp(data.improper_style,"harmonic") == 0) {
|
||||
|
||||
data.improper_harmonic_k = new double[data.nimpropertypes+1];
|
||||
data.improper_harmonic_chi = new double[data.nimpropertypes+1];
|
||||
fread(&data.improper_harmonic_k[1],sizeof(double),data.nimpropertypes,fp);
|
||||
fread(&data.improper_harmonic_chi[1],sizeof(double),
|
||||
data.nimpropertypes,fp);
|
||||
nread_double(&data.improper_harmonic_k[1],data.nimpropertypes,fp);
|
||||
nread_double(&data.improper_harmonic_chi[1],data.nimpropertypes,fp);
|
||||
|
||||
} else if (strcmp(data.improper_style,"hybrid") == 0) {
|
||||
|
||||
|
|
@ -4138,12 +4099,27 @@ void strip_suffix(char *style)
|
|||
|
||||
// ---------------------------------------------------------------------
|
||||
// binary reads from restart file
|
||||
// all are wrappers on fread()
|
||||
// perform endian swap if swapflag is set
|
||||
// ---------------------------------------------------------------------
|
||||
|
||||
void nread_int(int *buf, int n, FILE *fp)
|
||||
{
|
||||
fread(buf,sizeof(int),n,fp);
|
||||
if (swapflag) {}
|
||||
}
|
||||
|
||||
void nread_double(double *buf, int n, FILE *fp)
|
||||
{
|
||||
fread(buf,sizeof(double),n,fp);
|
||||
if (swapflag) {}
|
||||
}
|
||||
|
||||
int read_int(FILE *fp)
|
||||
{
|
||||
int value;
|
||||
fread(&value,sizeof(int),1,fp);
|
||||
if (swapflag) {}
|
||||
return value;
|
||||
}
|
||||
|
||||
|
|
@ -4151,6 +4127,7 @@ double read_double(FILE *fp)
|
|||
{
|
||||
double value;
|
||||
fread(&value,sizeof(double),1,fp);
|
||||
if (swapflag) {}
|
||||
return value;
|
||||
}
|
||||
|
||||
|
|
@ -4158,9 +4135,11 @@ char *read_char(FILE *fp)
|
|||
{
|
||||
int n;
|
||||
fread(&n,sizeof(int),1,fp);
|
||||
if (swapflag) {}
|
||||
if (n == 0) return NULL;
|
||||
char *value = new char[n];
|
||||
fread(value,sizeof(char),n,fp);
|
||||
if (swapflag) {}
|
||||
return value;
|
||||
}
|
||||
|
||||
|
|
@ -4168,5 +4147,29 @@ bigint read_bigint(FILE *fp)
|
|||
{
|
||||
bigint value;
|
||||
fread(&value,sizeof(bigint),1,fp);
|
||||
if (swapflag) {}
|
||||
return value;
|
||||
}
|
||||
|
||||
// ---------------------------------------------------------------------
|
||||
// auto-detect if restart file needs to be byte-swapped on this platform
|
||||
// return 0 if not, 1 if it does
|
||||
// re-open file with fp after checking first few bytes
|
||||
// ---------------------------------------------------------------------
|
||||
|
||||
int autodetect(FILE **pfp, char *file)
|
||||
{
|
||||
FILE *fp = *pfp;
|
||||
|
||||
// read, check, set return flag
|
||||
|
||||
int flag = 0;
|
||||
|
||||
// reset file pointer
|
||||
|
||||
fclose(fp);
|
||||
fp = fopen(file,"rb");
|
||||
*pfp = fp;
|
||||
|
||||
return flag;
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue