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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6656 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2011-08-08 23:10:20 +00:00
parent 82483909df
commit 1ce29fc9a1
1 changed files with 109 additions and 1 deletions
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110
tools/restart2data.cpp
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@ -141,6 +141,10 @@ class Data {
double *bond_feneexpand_epsilon,*bond_feneexpand_sigma;
double *bond_feneexpand_shift;
double *bond_harmonic_k,*bond_harmonic_r0;
double *bond_harmonicshift_umin,*bond_harmonicshift_r0,
*bond_harmonicshift_rc;
double *bond_harmonicshiftcut_umin,*bond_harmonicshiftcut_r0,
*bond_harmonicshiftcut_rc;
double *bond_morse_d0,*bond_morse_alpha,*bond_morse_r0;
double *bond_nonlinear_epsilon,*bond_nonlinear_r0,*bond_nonlinear_lamda;
double *bond_quartic_k,*bond_quartic_b1,*bond_quartic_b2;
@ -157,6 +161,11 @@ class Data {
double *angle_cosine_squared_k,*angle_cosine_squared_theta0;
double *angle_harmonic_k,*angle_harmonic_theta0;
double *angle_cg_cmm_epsilon,*angle_cg_cmm_sigma;
double *angle_cosineshift_umin,*angle_cosineshift_sint,
*angle_cosineshift_cost,*angle_cosineshift_theta0;
double *angle_cosineshiftexp_umin,*angle_cosineshiftexp_a,
*angle_cosineshiftexp_sint,*angle_cosineshiftexp_cost,
*angle_cosineshiftexp_theta0;
int *angle_cg_cmm_type;
double *dihedral_charmm_k,*dihedral_charmm_weight;
@ -184,6 +193,9 @@ class Data {
double *dihedral_multi_a4,*dihedral_multi_a5;
double *dihedral_opls_k1,*dihedral_opls_k2;
double *dihedral_opls_k3,*dihedral_opls_k4;
double *dihedral_cosineshiftexp_umin, *dihedral_cosineshiftexp_a,
*dihedral_cosineshiftexp_sint,*dihedral_cosineshiftexp_cost,
*dihedral_cosineshiftexp_theta;
double *improper_class2_k0,*improper_class2_chi0;
double *improper_class2_aa_k1,*improper_class2_aa_k2,*improper_class2_aa_k3;
@ -830,7 +842,7 @@ int atom_angle(double *buf, Data &data, int iatoms)
for (int k = 0; k < n; k++) {
type = static_cast<int> (buf[m++]);
atom1 = static_cast<int> (buf[m++]);
if (data.newton_bond || data.tag[iatoms] < atom1) {
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;
@ -2258,6 +2270,25 @@ void bond(FILE *fp, Data &data)
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,"harmonicshift") == 0) {
data.bond_harmonicshift_umin = new double[data.nbondtypes+1];
data.bond_harmonicshift_r0 = new double[data.nbondtypes+1];
data.bond_harmonicshift_rc = new double[data.nbondtypes+1];
fread(&data.bond_harmonicshift_umin[1],sizeof(double),data.nbondtypes,fp);
fread(&data.bond_harmonicshift_r0[1],sizeof(double),data.nbondtypes,fp);
fread(&data.bond_harmonicshift_rc[1],sizeof(double),data.nbondtypes,fp);
} else if (strcmp(data.bond_style,"harmonicshiftcut") == 0) {
data.bond_harmonicshiftcut_umin = new double[data.nbondtypes+1];
data.bond_harmonicshiftcut_r0 = new double[data.nbondtypes+1];
data.bond_harmonicshiftcut_rc = new double[data.nbondtypes+1];
fread(&data.bond_harmonicshiftcut_umin[1],sizeof(double),
data.nbondtypes,fp);
fread(&data.bond_harmonicshiftcut_r0[1],sizeof(double),data.nbondtypes,fp);
fread(&data.bond_harmonicshiftcut_rc[1],sizeof(double),data.nbondtypes,fp);
} else if (strcmp(data.bond_style,"morse") == 0) {
data.bond_morse_d0 = new double[data.nbondtypes+1];
@ -2372,6 +2403,34 @@ void angle(FILE *fp, Data &data)
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,"cosineshift") == 0) {
data.angle_cosineshift_umin = new double[data.nangletypes+1];
fread(&data.angle_cosineshift_umin[1],sizeof(double),data.nangletypes,fp);
data.angle_cosineshift_cost = new double[data.nangletypes+1];
fread(&data.angle_cosineshift_cost[1],sizeof(double),data.nangletypes,fp);
data.angle_cosineshift_sint = new double[data.nangletypes+1];
fread(&data.angle_cosineshift_sint[1],sizeof(double),data.nangletypes,fp);
data.angle_cosineshift_theta0 = new double[data.nangletypes+1];
fread(&data.angle_cosineshift_theta0[1],sizeof(double),data.nangletypes,fp);
} else if (strcmp(data.angle_style,"cosineshiftexp") == 0) {
data.angle_cosineshiftexp_umin = new double[data.nangletypes+1];
fread(&data.angle_cosineshiftexp_umin[1],sizeof(double),
data.nangletypes,fp);
data.angle_cosineshiftexp_a = new double[data.nangletypes+1];
fread(&data.angle_cosineshiftexp_a[1],sizeof(double),data.nangletypes,fp);
data.angle_cosineshiftexp_cost = new double[data.nangletypes+1];
fread(&data.angle_cosineshiftexp_cost[1],sizeof(double),
data.nangletypes,fp);
data.angle_cosineshiftexp_sint = new double[data.nangletypes+1];
fread(&data.angle_cosineshiftexp_sint[1],sizeof(double),
data.nangletypes,fp);
data.angle_cosineshiftexp_theta0 = new double[data.nangletypes+1];
fread(&data.angle_cosineshiftexp_theta0[1],sizeof(double),
data.nangletypes,fp);
} else if (strcmp(data.angle_style,"cosine") == 0) {
data.angle_cosine_k = new double[data.nangletypes+1];
@ -2582,6 +2641,24 @@ void dihedral(FILE *fp, Data &data)
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,"cosineshiftexp") == 0) {
data.dihedral_cosineshiftexp_umin = new double[data.ndihedraltypes+1];
fread(&data.dihedral_cosineshiftexp_umin[1],sizeof(double),
data.ndihedraltypes,fp);
data.dihedral_cosineshiftexp_a = new double[data.ndihedraltypes+1];
fread(&data.dihedral_cosineshiftexp_a[1],sizeof(double),
data.ndihedraltypes,fp);
data.dihedral_cosineshiftexp_cost = new double[data.ndihedraltypes+1];
fread(&data.dihedral_cosineshiftexp_cost[1],sizeof(double),
data.ndihedraltypes,fp);
data.dihedral_cosineshiftexp_sint = new double[data.ndihedraltypes+1];
fread(&data.dihedral_cosineshiftexp_sint[1],sizeof(double),
data.ndihedraltypes,fp);
data.dihedral_cosineshiftexp_theta = new double[data.ndihedraltypes+1];
fread(&data.dihedral_cosineshiftexp_theta[1],sizeof(double),
data.ndihedraltypes,fp);
} else if (strcmp(data.dihedral_style,"table") == 0) {
@ -2967,6 +3044,18 @@ void Data::write(FILE *fp, FILE *fp2)
fprintf(fp,"%d %g %g\n",i,
bond_harmonic_k[i],bond_harmonic_r0[i]);
} else if (strcmp(bond_style,"harmonicshift") == 0) {
for (int i = 1; i <= nbondtypes; i++)
fprintf(fp,"%d %g %g %g\n",i,
bond_harmonicshift_umin[i],bond_harmonicshift_r0[i],
bond_harmonicshift_rc[i]);
} else if (strcmp(bond_style,"harmonicshiftcut") == 0) {
for (int i = 1; i <= nbondtypes; i++)
fprintf(fp,"%d %g %g %g\n",i,
bond_harmonicshiftcut_umin[i],bond_harmonicshiftcut_r0[i],
bond_harmonicshiftcut_rc[i]);
} else if (strcmp(bond_style,"morse") == 0) {
for (int i = 1; i <= nbondtypes; i++)
fprintf(fp,"%d %g %g %g\n",i,
@ -3038,6 +3127,17 @@ void Data::write(FILE *fp, FILE *fp2)
for (int i = 1; i <= nangletypes; i++)
fprintf(fp,"%d %g\n",i,angle_cosine_k[i]);
} else if (strcmp(angle_style,"cosineshift") == 0) {
for (int i = 1; i <= nangletypes; i++)
fprintf(fp,"%d %g %g\n",i,angle_cosineshift_umin[i],
angle_cosineshift_theta0[i]/PI*180.0);
} else if (strcmp(angle_style,"cosineshiftexp") == 0) {
for (int i = 1; i <= nangletypes; i++)
fprintf(fp,"%d %g %g %g\n",i,angle_cosineshiftexp_umin[i],
angle_cosineshiftexp_theta0[i]/PI*180.0,
angle_cosineshiftexp_a[i]);
} else if ((strcmp(angle_style,"cosine/squared") == 0) ||
(strcmp(angle_style,"cosine/delta") == 0)) {
for (int i = 1; i <= nangletypes; i++)
@ -3156,6 +3256,14 @@ void Data::write(FILE *fp, FILE *fp2)
dihedral_harmonic_k[i],dihedral_harmonic_multiplicity[i],
dihedral_harmonic_sign[i]);
} else if (strcmp(dihedral_style,"cosineshiftexp") == 0) {
for (int i = 1; i <= ndihedraltypes; i++)
fprintf(fp,"%d %g %g %g\n",i,
dihedral_cosineshiftexp_umin[i],
dihedral_cosineshiftexp_theta[i]*180.0/PI,
dihedral_cosineshiftexp_a[i]
);
} else if (strcmp(dihedral_style,"helix") == 0) {
for (int i = 1; i <= ndihedraltypes; i++)
fprintf(fp,"%d %g %g %g\n",i,dihedral_helix_aphi[i],