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lammps/src/molecule.cpp
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molecule.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "stdlib.h"
#include "string.h"
#include "molecule.h"
#include "atom.h"
#include "atom_vec.h"
#include "force.h"
#include "comm.h"
#include "domain.h"
#include "math_extra.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define MAXLINE 256
#define EPSILON 1.0e-7
#define BIG 1.0e20
/* ---------------------------------------------------------------------- */
Molecule::Molecule(LAMMPS *lmp, char *idarg, char *file) : Pointers(lmp)
{
me = comm->me;
int n = strlen(idarg) + 1;
id = new char[n];
strcpy(id,idarg);
for (int i = 0; i < n-1; i++)
if (!isalnum(id[i]) && id[i] != '_')
error->all(FLERR,"Molecule template ID must be "
"alphanumeric or underscore characters");
// initialize all fields to empty
initialize();
// scan file for sizes of all fields and allocate them
if (me == 0) open(file);
read(0);
if (me == 0) fclose(fp);
allocate();
// read file again to populate all fields
if (me == 0) open(file);
read(1);
if (me == 0) fclose(fp);
// stats
if (me == 0) {
if (screen)
fprintf(screen,"Read molecule %s:\n"
" %d atoms with %d types\n %d bonds with %d types\n"
" %d angles with %d types\n %d dihedrals with %d types\n"
" %d impropers with %d types\n",
id,natoms,ntypes,
nbonds,nbondtypes,nangles,nangletypes,
ndihedrals,ndihedraltypes,nimpropers,nimpropertypes);
if (logfile)
fprintf(logfile,"Read molecule %s:\n"
" %d atoms with %d types\n %d bonds with %d types\n"
" %d angles with %d types\n %d dihedrals with %d types\n"
" %d impropers with %d types\n",
id,natoms,ntypes,
nbonds,nbondtypes,nangles,nangletypes,
ndihedrals,ndihedraltypes,nimpropers,nimpropertypes);
}
}
/* ---------------------------------------------------------------------- */
Molecule::~Molecule()
{
delete [] id;
deallocate();
}
/* ----------------------------------------------------------------------
compute center = geometric center of molecule
also compute:
dx = displacement of each atom from center
molradius = radius of molecule from center including finite-size particles
------------------------------------------------------------------------- */
void Molecule::compute_center()
{
if (centerflag) return;
centerflag = 1;
center[0] = center[1] = center[2] = 0.0;
for (int i = 0; i < natoms; i++) {
center[0] += x[i][0];
center[1] += x[i][1];
center[2] += x[i][2];
}
center[0] /= natoms;
center[1] /= natoms;
center[2] /= natoms;
memory->destroy(dx);
memory->create(dx,natoms,3,"molecule:dx");
for (int i = 0; i < natoms; i++) {
dx[i][0] = x[i][0] - center[0];
dx[i][1] = x[i][1] - center[1];
dx[i][2] = x[i][2] - center[2];
}
molradius = 0.0;
for (int i = 0; i < natoms; i++) {
double rad = MathExtra::len3(dx[i]);
if (radiusflag) rad += radius[i];
molradius = MAX(molradius,rad);
}
}
/* ----------------------------------------------------------------------
compute masstotal = total mass of molecule
could have been set by user, otherwise calculate it
------------------------------------------------------------------------- */
void Molecule::compute_mass()
{
if (massflag) return;
massflag = 1;
if (!rmassflag) atom->check_mass();
masstotal = 0.0;
for (int i = 0; i < natoms; i++) {
if (rmassflag) masstotal += rmass[i];
else masstotal += atom->mass[type[i]];
}
}
/* ----------------------------------------------------------------------
compute com = center of mass of molecule
could have been set by user, otherwise calculate it
NOTE: account for finite size particles?
also compute:
dxcom = displacement of each atom from COM
comatom = which atom (1-Natom) is nearest the COM
maxextent = furthest any atom in molecule is from comatom (not COM)
------------------------------------------------------------------------- */
void Molecule::compute_com()
{
if (!comflag) {
comflag = 1;
if (!rmassflag) atom->check_mass();
double onemass;
com[0] = com[1] = com[2] = 0.0;
for (int i = 0; i < natoms; i++) {
if (rmassflag) onemass = rmass[i];
else onemass = atom->mass[type[i]];
com[0] += x[i][0]*onemass;
com[1] += x[i][1]*onemass;
com[2] += x[i][2]*onemass;
}
com[0] /= masstotal;
com[1] /= masstotal;
com[2] /= masstotal;
}
memory->destroy(dxcom);
memory->create(dxcom,natoms,3,"molecule:dxcom");
for (int i = 0; i < natoms; i++) {
dxcom[i][0] = x[i][0] - com[0];
dxcom[i][1] = x[i][1] - com[1];
dxcom[i][2] = x[i][2] - com[2];
}
double rsqmin = BIG;
for (int i = 0; i < natoms; i++) {
double rsq = MathExtra::lensq3(dxcom[i]);
if (rsq < rsqmin) {
comatom = i;
rsqmin = rsq;
}
}
double rsqmax = 0.0;
for (int i = 0; i < natoms; i++) {
double dx = x[comatom][0] - x[i][0];
double dy = x[comatom][1] - x[i][1];
double dz = x[comatom][2] - x[i][2];
double rsq = dx*dx + dy*dy + dz*dz;
rsqmax = MAX(rsqmax,rsq);
}
comatom++;
maxextent = sqrt(rsqmax);
}
/* ----------------------------------------------------------------------
compute itensor = 6 moments of inertia of molecule around xyz axes
could have been set by user, otherwise calculate it
NOTE: account for finite size particles?
also compute:
inertia = 3 principal components of inertia
ex,ey,ez = principal axes in space coords
quat = quaternion for orientation of molecule
dxbody = displacement of each atom from COM in body frame
------------------------------------------------------------------------- */
void Molecule::compute_inertia()
{
if (!inertiaflag) {
inertiaflag = 1;
if (!rmassflag) atom->check_mass();
double onemass,dx,dy,dz;
for (int i = 0; i < 6; i++) itensor[i] = 0.0;
for (int i = 0; i < natoms; i++) {
if (rmassflag) onemass = rmass[i];
else onemass = atom->type[type[i]];
dx = dxcom[i][0];
dy = dxcom[i][1];
dz = dxcom[i][2];
itensor[0] += onemass * (dy*dy + dz*dz);
itensor[1] += onemass * (dx*dx + dz*dz);
itensor[2] += onemass * (dx*dx + dy*dy);
itensor[3] -= onemass * dy*dz;
itensor[4] -= onemass * dx*dz;
itensor[5] -= onemass * dx*dy;
}
}
// diagonalize inertia tensor for each body via Jacobi rotations
// inertia = 3 eigenvalues = principal moments of inertia
// evectors and exzy = 3 evectors = principal axes of rigid body
double cross[3];
double tensor[3][3],evectors[3][3];
tensor[0][0] = itensor[0];
tensor[1][1] = itensor[1];
tensor[2][2] = itensor[2];
tensor[1][2] = tensor[2][1] = itensor[3];
tensor[0][2] = tensor[2][0] = itensor[4];
tensor[0][1] = tensor[1][0] = itensor[5];
if (MathExtra::jacobi(tensor,inertia,evectors))
error->all(FLERR,"Insufficient Jacobi rotations for rigid molecule");
ex[0] = evectors[0][0];
ex[1] = evectors[1][0];
ex[2] = evectors[2][0];
ey[0] = evectors[0][1];
ey[1] = evectors[1][1];
ey[2] = evectors[2][1];
ez[0] = evectors[0][2];
ez[1] = evectors[1][2];
ez[2] = evectors[2][2];
// if any principal moment < scaled EPSILON, set to 0.0
double max;
max = MAX(inertia[0],inertia[1]);
max = MAX(max,inertia[2]);
if (inertia[0] < EPSILON*max) inertia[0] = 0.0;
if (inertia[1] < EPSILON*max) inertia[1] = 0.0;
if (inertia[2] < EPSILON*max) inertia[2] = 0.0;
// enforce 3 evectors as a right-handed coordinate system
// flip 3rd vector if needed
MathExtra::cross3(ex,ey,cross);
if (MathExtra::dot3(cross,ez) < 0.0) MathExtra::negate3(ez);
// create quaternion
MathExtra::exyz_to_q(ex,ey,ez,quat);
// compute displacements in body frame defined by quat
memory->destroy(dxbody);
memory->create(dxbody,natoms,3,"molecule:dxbody");
for (int i = 0; i < natoms; i++)
MathExtra::transpose_matvec(ex,ey,ez,dxcom[i],dxbody[i]);
}
/* ----------------------------------------------------------------------
read molecule info from file
flag = 0, just scan for sizes of fields
flag = 1, read and store fields
------------------------------------------------------------------------- */
void Molecule::read(int flag)
{
char line[MAXLINE],keyword[MAXLINE];
char *eof,*ptr;
// skip 1st line of file
if (me == 0) {
eof = fgets(line,MAXLINE,fp);
if (eof == NULL) error->one(FLERR,"Unexpected end of molecule file");
}
// read header lines
// skip blank lines or lines that start with "#"
// stop when read an unrecognized line
while (1) {
readline(line);
// trim anything from '#' onward
// if line is blank, continue
if ((ptr = strchr(line,'#'))) *ptr = '\0';
if (strspn(line," \t\n\r") == strlen(line)) continue;
// search line for header keywords and set corresponding variable
if (strstr(line,"atoms")) sscanf(line,"%d",&natoms);
else if (strstr(line,"bonds")) sscanf(line,"%d",&nbonds);
else if (strstr(line,"angles")) sscanf(line,"%d",&nangles);
else if (strstr(line,"dihedrals")) sscanf(line,"%d",&ndihedrals);
else if (strstr(line,"impropers")) sscanf(line,"%d",&nimpropers);
else if (strstr(line,"mass")) {
massflag = 1;
sscanf(line,"%lg",&masstotal);
}
else if (strstr(line,"com")) {
comflag = 1;
sscanf(line,"%lg %lg %lg",&com[0],&com[1],&com[2]);
if (domain->dimension == 2 && com[2] != 0.0)
error->all(FLERR,"Molecule file z center-of-mass must be 0.0 for 2d");
}
else if (strstr(line,"inertia")) {
inertiaflag = 1;
sscanf(line,"%lg %lg %lg %lg %lg %lg",
&itensor[0],&itensor[1],&itensor[2],
&itensor[3],&itensor[4],&itensor[5]);
}
else break;
}
// error check
if (flag == 0) {
if (natoms == 0) error->all(FLERR,"No atom count in molecule file");
}
// count = vector for tallying bonds,angles,etc per atom
if (flag == 0) memory->create(count,natoms,"molecule:count");
else count = NULL;
// grab keyword and skip next line
parse_keyword(0,line,keyword);
readline(line);
// loop over sections of molecule file
while (strlen(keyword)) {
if (strcmp(keyword,"Coords") == 0) {
xflag = 1;
if (flag) coords(line);
else skip_lines(natoms,line);
} else if (strcmp(keyword,"Types") == 0) {
typeflag = 1;
if (flag) types(line);
else skip_lines(natoms,line);
} else if (strcmp(keyword,"Charges") == 0) {
qflag = 1;
if (flag) charges(line);
else skip_lines(natoms,line);
} else if (strcmp(keyword,"Diameters") == 0) {
radiusflag = 1;
if (flag) diameters(line);
else skip_lines(natoms,line);
} else if (strcmp(keyword,"Masses") == 0) {
rmassflag = 1;
if (flag) masses(line);
else skip_lines(natoms,line);
} else if (strcmp(keyword,"Bonds") == 0) {
if (nbonds == 0)
error->all(FLERR,"Molecule file has bonds but no nbonds setting");
bondflag = tag_require = 1;
bonds(flag,line);
} else if (strcmp(keyword,"Angles") == 0) {
if (nangles == 0)
error->all(FLERR,"Molecule file has angles but no nangles setting");
angleflag = tag_require = 1;
angles(flag,line);
} else if (strcmp(keyword,"Dihedrals") == 0) {
if (ndihedrals == 0) error->all(FLERR,"Molecule file has dihedrals "
"but no ndihedrals setting");
dihedralflag = tag_require = 1;
dihedrals(flag,line);
} else if (strcmp(keyword,"Impropers") == 0) {
if (nimpropers == 0) error->all(FLERR,"Molecule file has impropers "
"but no nimpropers setting");
improperflag = tag_require = 1;
impropers(flag,line);
} else if (strcmp(keyword,"Special Bond Counts") == 0) {
nspecialflag = 1;
nspecial_read(flag,line);
} else if (strcmp(keyword,"Special Bonds") == 0) {
specialflag = tag_require = 1;
if (flag) special_read(line);
else skip_lines(natoms,line);
} else if (strcmp(keyword,"Shake Flags") == 0) {
shakeflagflag = 1;
if (flag) shakeflag_read(line);
else skip_lines(natoms,line);
} else if (strcmp(keyword,"Shake Atoms") == 0) {
shakeatomflag = tag_require = 1;
if (shaketypeflag) shakeflag = 1;
if (!shakeflagflag)
error->all(FLERR,"Molecule file shake flags not before shake atoms");
if (flag) shakeatom_read(line);
else skip_lines(natoms,line);
} else if (strcmp(keyword,"Shake Bond Types") == 0) {
shaketypeflag = 1;
if (shakeatomflag) shakeflag = 1;
if (!shakeflagflag)
error->all(FLERR,"Molecule file shake flags not before shake bonds");
if (flag) shaketype_read(line);
else skip_lines(natoms,line);
} else error->one(FLERR,"Unknown section in molecule file");
parse_keyword(1,line,keyword);
}
// clean up
memory->destroy(count);
// error check
if (flag == 0) {
if ((nspecialflag && !specialflag) || (!nspecialflag && specialflag))
error->all(FLERR,"Molecule file needs both Special Bond sections");
if (specialflag && !bondflag)
error->all(FLERR,"Molecule file has special flags but no bonds");
if (!specialflag && bondflag)
error->all(FLERR,"Molecule file has bonds but no special flags");
if ((shakeflagflag || shakeatomflag || shaketypeflag) && !shakeflag)
error->all(FLERR,"Molecule file shake info is incomplete");
}
}
/* ----------------------------------------------------------------------
read coords from file
------------------------------------------------------------------------- */
void Molecule::coords(char *line)
{
int tmp;
for (int i = 0; i < natoms; i++) {
readline(line);
sscanf(line,"%d %lg %lg %lg",&tmp,&x[i][0],&x[i][1],&x[i][2]);
}
if (domain->dimension == 2) {
for (int i = 0; i < natoms; i++)
if (x[i][2] != 0.0)
error->all(FLERR,"Molecule file z coord must be 0.0 for 2d");
}
}
/* ----------------------------------------------------------------------
read types from file
set ntypes = max of any atom type
------------------------------------------------------------------------- */
void Molecule::types(char *line)
{
int tmp;
for (int i = 0; i < natoms; i++) {
readline(line);
sscanf(line,"%d %d",&tmp,&type[i]);
}
for (int i = 0; i < natoms; i++)
if (type[i] <= 0)
error->all(FLERR,"Invalid atom type in molecule file");
for (int i = 0; i < natoms; i++)
ntypes = MAX(ntypes,type[i]);
}
/* ----------------------------------------------------------------------
read charges from file
------------------------------------------------------------------------- */
void Molecule::charges(char *line)
{
int tmp;
for (int i = 0; i < natoms; i++) {
readline(line);
sscanf(line,"%d %lg",&tmp,&q[i]);
}
}
/* ----------------------------------------------------------------------
read diameters from file and set radii
------------------------------------------------------------------------- */
void Molecule::diameters(char *line)
{
int tmp;
for (int i = 0; i < natoms; i++) {
readline(line);
sscanf(line,"%d %lg",&tmp,&radius[i]);
radius[i] *= 0.5;
}
for (int i = 0; i < natoms; i++)
if (radius[i] < 0.0)
error->all(FLERR,"Invalid atom diameter in molecule file");
}
/* ----------------------------------------------------------------------
read masses from file
------------------------------------------------------------------------- */
void Molecule::masses(char *line)
{
int tmp;
for (int i = 0; i < natoms; i++) {
readline(line);
sscanf(line,"%d %lg",&tmp,&rmass[i]);
}
for (int i = 0; i < natoms; i++)
if (rmass[i] <= 0.0) error->all(FLERR,"Invalid atom mass in molecule file");
}
/* ----------------------------------------------------------------------
read bonds from file
set nbondtypes = max type of any bond
store each with both atoms if newton_bond = 0
if flag = 0, just count bonds/atom
if flag = 1, store them with atoms
------------------------------------------------------------------------- */
void Molecule::bonds(int flag, char *line)
{
int tmp,itype;
tagint m,atom1,atom2;
int newton_bond = force->newton_bond;
if (flag == 0)
for (int i = 0; i < natoms; i++) count[i] = 0;
else
for (int i = 0; i < natoms; i++) num_bond[i] = 0;
for (int i = 0; i < nbonds; i++) {
readline(line);
sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&itype,&atom1,&atom2);
if (atom1 <= 0 || atom1 > natoms ||
atom2 <= 0 || atom2 > natoms)
error->one(FLERR,"Invalid atom ID in Bonds section of molecule file");
if (itype <= 0)
error->one(FLERR,"Invalid bond type in Bonds section of molecule file");
if (flag) {
m = atom1-1;
nbondtypes = MAX(nbondtypes,itype);
bond_type[m][num_bond[m]] = itype;
bond_atom[m][num_bond[m]] = atom2;
num_bond[m]++;
if (newton_bond == 0) {
m = atom2-1;
bond_type[m][num_bond[m]] = itype;
bond_atom[m][num_bond[m]] = atom1;
num_bond[m]++;
}
} else {
count[atom1-1]++;
if (newton_bond == 0) count[atom2-1]++;
}
}
// bond_per_atom = max of count vector
if (flag == 0) {
bond_per_atom = 0;
for (int i = 0; i < natoms; i++)
bond_per_atom = MAX(bond_per_atom,count[i]);
}
}
/* ----------------------------------------------------------------------
read angles from file
store each with all 3 atoms if newton_bond = 0
if flag = 0, just count angles/atom
if flag = 1, store them with atoms
------------------------------------------------------------------------- */
void Molecule::angles(int flag, char *line)
{
int tmp,itype;
tagint m,atom1,atom2,atom3;
int newton_bond = force->newton_bond;
if (flag == 0)
for (int i = 0; i < natoms; i++) count[i] = 0;
else
for (int i = 0; i < natoms; i++) num_angle[i] = 0;
for (int i = 0; i < nangles; i++) {
readline(line);
sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&itype,&atom1,&atom2,&atom3);
if (atom1 <= 0 || atom1 > natoms ||
atom2 <= 0 || atom2 > natoms ||
atom3 <= 0 || atom3 > natoms)
error->one(FLERR,"Invalid atom ID in Angles section of molecule file");
if (itype <= 0)
error->one(FLERR,"Invalid angle type in Angles section of molecule file");
if (flag) {
m = atom2-1;
nangletypes = MAX(nangletypes,itype);
angle_type[m][num_angle[m]] = itype;
angle_atom1[m][num_angle[m]] = atom1;
angle_atom2[m][num_angle[m]] = atom2;
angle_atom3[m][num_angle[m]] = atom3;
num_angle[m]++;
if (newton_bond == 0) {
m = atom1-1;
angle_type[m][num_angle[m]] = itype;
angle_atom1[m][num_angle[m]] = atom1;
angle_atom2[m][num_angle[m]] = atom2;
angle_atom3[m][num_angle[m]] = atom3;
num_angle[m]++;
m = atom3-1;
angle_type[m][num_angle[m]] = itype;
angle_atom1[m][num_angle[m]] = atom1;
angle_atom2[m][num_angle[m]] = atom2;
angle_atom3[m][num_angle[m]] = atom3;
num_angle[m]++;
}
} else {
count[atom2-1]++;
if (newton_bond == 0) {
count[atom1-1]++;
count[atom3-1]++;
}
}
}
// angle_per_atom = max of count vector
if (flag == 0) {
angle_per_atom = 0;
for (int i = 0; i < natoms; i++)
angle_per_atom = MAX(angle_per_atom,count[i]);
}
}
/* ----------------------------------------------------------------------
read dihedrals from file
store each with all 4 atoms if newton_bond = 0
if flag = 0, just count dihedrals/atom
if flag = 1, store them with atoms
------------------------------------------------------------------------- */
void Molecule::dihedrals(int flag, char *line)
{
int tmp,itype;
tagint m,atom1,atom2,atom3,atom4;
int newton_bond = force->newton_bond;
if (flag == 0)
for (int i = 0; i < natoms; i++) count[i] = 0;
else
for (int i = 0; i < natoms; i++) num_dihedral[i] = 0;
for (int i = 0; i < ndihedrals; i++) {
readline(line);
sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT " ",
&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
if (atom1 <= 0 || atom1 > natoms ||
atom2 <= 0 || atom2 > natoms ||
atom3 <= 0 || atom3 > natoms ||
atom4 <= 0 || atom4 > natoms)
error->one(FLERR,
"Invalid atom ID in dihedrals section of molecule file");
if (itype <= 0)
error->one(FLERR,
"Invalid dihedral type in dihedrals section of molecule file");
if (flag) {
m = atom2-1;
ndihedraltypes = MAX(ndihedraltypes,itype);
dihedral_type[m][num_dihedral[m]] = itype;
dihedral_atom1[m][num_dihedral[m]] = atom1;
dihedral_atom2[m][num_dihedral[m]] = atom2;
dihedral_atom3[m][num_dihedral[m]] = atom3;
dihedral_atom4[m][num_dihedral[m]] = atom4;
num_dihedral[m]++;
if (newton_bond == 0) {
m = atom1-1;
dihedral_type[m][num_dihedral[m]] = itype;
dihedral_atom1[m][num_dihedral[m]] = atom1;
dihedral_atom2[m][num_dihedral[m]] = atom2;
dihedral_atom3[m][num_dihedral[m]] = atom3;
dihedral_atom4[m][num_dihedral[m]] = atom4;
num_dihedral[m]++;
m = atom3-1;
dihedral_type[m][num_dihedral[m]] = itype;
dihedral_atom1[m][num_dihedral[m]] = atom1;
dihedral_atom2[m][num_dihedral[m]] = atom2;
dihedral_atom3[m][num_dihedral[m]] = atom3;
dihedral_atom4[m][num_dihedral[m]] = atom4;
num_dihedral[m]++;
m = atom4-1;
dihedral_type[m][num_dihedral[m]] = itype;
dihedral_atom1[m][num_dihedral[m]] = atom1;
dihedral_atom2[m][num_dihedral[m]] = atom2;
dihedral_atom3[m][num_dihedral[m]] = atom3;
dihedral_atom4[m][num_dihedral[m]] = atom4;
num_dihedral[m]++;
}
} else {
count[atom2-1]++;
if (newton_bond == 0) {
count[atom1-1]++;
count[atom3-1]++;
count[atom4-1]++;
}
}
}
// dihedral_per_atom = max of count vector
if (flag == 0) {
dihedral_per_atom = 0;
for (int i = 0; i < natoms; i++)
dihedral_per_atom = MAX(dihedral_per_atom,count[i]);
}
}
/* ----------------------------------------------------------------------
read impropers from file
store each with all 4 atoms if newton_bond = 0
if flag = 0, just count impropers/atom
if flag = 1, store them with atoms
------------------------------------------------------------------------- */
void Molecule::impropers(int flag, char *line)
{
int tmp,itype;
tagint m,atom1,atom2,atom3,atom4;
int newton_bond = force->newton_bond;
if (flag == 0)
for (int i = 0; i < natoms; i++) count[i] = 0;
else
for (int i = 0; i < natoms; i++) num_improper[i] = 0;
for (int i = 0; i < nimpropers; i++) {
readline(line);
sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT " ",
&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
if (atom1 <= 0 || atom1 > natoms ||
atom2 <= 0 || atom2 > natoms ||
atom3 <= 0 || atom3 > natoms ||
atom4 <= 0 || atom4 > natoms)
error->one(FLERR,
"Invalid atom ID in impropers section of molecule file");
if (itype <= 0)
error->one(FLERR,
"Invalid improper type in impropers section of molecule file");
if (flag) {
m = atom2-1;
nimpropertypes = MAX(nimpropertypes,itype);
improper_type[m][num_improper[m]] = itype;
improper_atom1[m][num_improper[m]] = atom1;
improper_atom2[m][num_improper[m]] = atom2;
improper_atom3[m][num_improper[m]] = atom3;
improper_atom4[m][num_improper[m]] = atom4;
num_improper[m]++;
if (newton_bond == 0) {
m = atom1-1;
improper_type[m][num_improper[m]] = itype;
improper_atom1[m][num_improper[m]] = atom1;
improper_atom2[m][num_improper[m]] = atom2;
improper_atom3[m][num_improper[m]] = atom3;
improper_atom4[m][num_improper[m]] = atom4;
num_improper[m]++;
m = atom3-1;
improper_type[m][num_improper[m]] = itype;
improper_atom1[m][num_improper[m]] = atom1;
improper_atom2[m][num_improper[m]] = atom2;
improper_atom3[m][num_improper[m]] = atom3;
improper_atom4[m][num_improper[m]] = atom4;
num_improper[m]++;
m = atom4-1;
improper_type[m][num_improper[m]] = itype;
improper_atom1[m][num_improper[m]] = atom1;
improper_atom2[m][num_improper[m]] = atom2;
improper_atom3[m][num_improper[m]] = atom3;
improper_atom4[m][num_improper[m]] = atom4;
num_improper[m]++;
}
} else {
count[atom2-1]++;
if (newton_bond == 0) {
count[atom1-1]++;
count[atom3-1]++;
count[atom4-1]++;
}
}
}
// improper_per_atom = max of count vector
if (flag == 0) {
improper_per_atom = 0;
for (int i = 0; i < natoms; i++)
improper_per_atom = MAX(improper_per_atom,count[i]);
}
}
/* ----------------------------------------------------------------------
read 3 special bonds counts from file
if flag = 0, just tally maxspecial
if flag = 1, store them with atoms
------------------------------------------------------------------------- */
void Molecule::nspecial_read(int flag, char *line)
{
int tmp,c1,c2,c3;
if (flag == 0) maxspecial = 0;
for (int i = 0; i < natoms; i++) {
readline(line);
sscanf(line,"%d %d %d %d",&tmp,&c1,&c2,&c3);
if (flag) {
nspecial[i][0] = c1;
nspecial[i][1] = c1+c2;
nspecial[i][2] = c1+c2+c3;
} else maxspecial = MAX(maxspecial,c1+c2+c3);
}
}
/* ----------------------------------------------------------------------
read special bond indices from file
------------------------------------------------------------------------- */
void Molecule::special_read(char *line)
{
int m,nwords;
char **words = new char*[maxspecial+1];
for (int i = 0; i < natoms; i++) {
readline(line);
nwords = parse(line,words,maxspecial+1);
if (nwords != nspecial[i][2]+1)
error->all(FLERR,"Molecule file special list "
"does not match special count");
for (m = 1; m < nwords; m++) {
special[i][m-1] = ATOTAGINT(words[m]);
if (special[i][m-1] <= 0 || special[i][m-1] > natoms ||
special[i][m-1] == i+1)
error->all(FLERR,"Invalid special atom index in molecule file");
}
}
delete [] words;
}
/* ----------------------------------------------------------------------
read SHAKE flags from file
------------------------------------------------------------------------- */
void Molecule::shakeflag_read(char *line)
{
int tmp;
for (int i = 0; i < natoms; i++) {
readline(line);
sscanf(line,"%d %d",&tmp,&shake_flag[i]);
}
for (int i = 0; i < natoms; i++)
if (shake_flag[i] < 0 || shake_flag[i] > 4)
error->all(FLERR,"Invalid shake flag in molecule file");
}
/* ----------------------------------------------------------------------
read SHAKE atom info from file
------------------------------------------------------------------------- */
void Molecule::shakeatom_read(char *line)
{
int tmp;
for (int i = 0; i < natoms; i++) {
readline(line);
if (shake_flag[i] == 1)
sscanf(line,"%d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&shake_atom[i][0],&shake_atom[i][1],&shake_atom[i][2]);
else if (shake_flag[i] == 2)
sscanf(line,"%d " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&shake_atom[i][0],&shake_atom[i][1]);
else if (shake_flag[i] == 3)
sscanf(line,"%d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&shake_atom[i][0],&shake_atom[i][1],&shake_atom[i][2]);
else if (shake_flag[i] == 4)
sscanf(line,"%d " TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&shake_atom[i][0],&shake_atom[i][1],
&shake_atom[i][2],&shake_atom[i][3]);
}
for (int i = 0; i < natoms; i++) {
int m = shake_flag[i];
if (m == 1) m = 3;
for (int j = 0; j < m; j++)
if (shake_atom[i][j] <= 0 || shake_atom[i][j] > natoms)
error->all(FLERR,"Invalid shake atom in molecule file");
}
}
/* ----------------------------------------------------------------------
read SHAKE bond type info from file
------------------------------------------------------------------------- */
void Molecule::shaketype_read(char *line)
{
int tmp;
for (int i = 0; i < natoms; i++) {
readline(line);
if (shake_flag[i] == 1)
sscanf(line,"%d %d %d %d",&tmp,
&shake_type[i][0],&shake_type[i][1],&shake_type[i][2]);
else if (shake_flag[i] == 2)
sscanf(line,"%d %d",&tmp,&shake_type[i][0]);
else if (shake_flag[i] == 3)
sscanf(line,"%d %d %d",&tmp,&shake_type[i][0],&shake_type[i][1]);
else if (shake_flag[i] == 4)
sscanf(line,"%d %d %d %d",&tmp,
&shake_type[i][0],&shake_type[i][1],&shake_type[i][2]);
}
for (int i = 0; i < natoms; i++) {
int m = shake_flag[i];
if (m == 1) m = 3;
for (int j = 0; j < m-1; j++)
if (shake_type[i][j] <= 0)
error->all(FLERR,"Invalid shake bond type in molecule file");
if (shake_flag[i] == 1)
if (shake_type[i][2] <= 0)
error->all(FLERR,"Invalid shake angle type in molecule file");
}
}
/* ----------------------------------------------------------------------
error check molecule attributes and topology against system settings
flag = 0, just check this molecule
flag = 1, check all molecules in set, this is 1st molecule in set
------------------------------------------------------------------------- */
void Molecule::check_attributes(int flag)
{
int n = 1;
if (flag) n = nset;
int imol = atom->find_molecule(id);
for (int i = imol; i < imol+n; i++) {
Molecule *onemol = atom->molecules[imol];
// check per-atom attributes of molecule
// warn if not a match
int mismatch = 0;
if (onemol->qflag && !atom->q_flag) mismatch = 1;
if (onemol->radiusflag && !atom->radius_flag) mismatch = 1;
if (onemol->rmassflag && !atom->rmass_flag) mismatch = 1;
if (mismatch && me == 0)
error->warning(FLERR,
"Molecule attributes do not match system attributes");
// for all atom styles, check nbondtype,etc
mismatch = 0;
if (atom->nbondtypes < onemol->nbondtypes) mismatch = 1;
if (atom->nangletypes < onemol->nangletypes) mismatch = 1;
if (atom->ndihedraltypes < onemol->ndihedraltypes) mismatch = 1;
if (atom->nimpropertypes < onemol->nimpropertypes) mismatch = 1;
if (mismatch)
error->all(FLERR,"Molecule topology type exceeds system topology type");
// for molecular atom styles, check bond_per_atom,etc + maxspecial
// do not check for atom style template, since nothing stored per atom
if (atom->molecular == 1) {
if (atom->avec->bonds_allow &&
atom->bond_per_atom < onemol->bond_per_atom) mismatch = 1;
if (atom->avec->angles_allow &&
atom->angle_per_atom < onemol->angle_per_atom) mismatch = 1;
if (atom->avec->dihedrals_allow &&
atom->dihedral_per_atom < onemol->dihedral_per_atom) mismatch = 1;
if (atom->avec->impropers_allow &&
atom->improper_per_atom < onemol->improper_per_atom) mismatch = 1;
if (atom->maxspecial < onemol->maxspecial) mismatch = 1;
if (mismatch)
error->all(FLERR,"Molecule toplogy/atom exceeds system topology/atom");
}
// warn if molecule topology defined but no special settings
if (onemol->bondflag && !onemol->specialflag)
if (me == 0) error->warning(FLERR,"Molecule has bond topology "
"but no special bond settings");
}
}
/* ----------------------------------------------------------------------
init all data structures to empty
------------------------------------------------------------------------- */
void Molecule::initialize()
{
natoms = 0;
nbonds = nangles = ndihedrals = nimpropers = 0;
ntypes = 0;
nbondtypes = nangletypes = ndihedraltypes = nimpropertypes = 0;
bond_per_atom = angle_per_atom = dihedral_per_atom = improper_per_atom = 0;
maxspecial = 0;
xflag = typeflag = qflag = radiusflag = rmassflag = 0;
bondflag = angleflag = dihedralflag = improperflag = 0;
nspecialflag = specialflag = 0;
shakeflag = shakeflagflag = shakeatomflag = shaketypeflag = 0;
centerflag = massflag = comflag = inertiaflag = 0;
tag_require = 0;
x = NULL;
type = NULL;
q = NULL;
radius = NULL;
rmass = NULL;
num_bond = NULL;
bond_type = NULL;
bond_atom = NULL;
num_angle = NULL;
angle_type = NULL;
angle_atom1 = angle_atom2 = angle_atom3 = NULL;
num_dihedral = NULL;
dihedral_type = NULL;
dihedral_atom1 = dihedral_atom2 = dihedral_atom3 = dihedral_atom4 = NULL;
num_improper = NULL;
improper_type = NULL;
improper_atom1 = improper_atom2 = improper_atom3 = improper_atom4 = NULL;
nspecial = NULL;
special = NULL;
shake_flag = NULL;
shake_atom = NULL;
shake_type = NULL;
dx = NULL;
dxcom = NULL;
dxbody = NULL;
}
/* ----------------------------------------------------------------------
allocate all data structures
also initialize values for data structures that are always allocated
------------------------------------------------------------------------- */
void Molecule::allocate()
{
if (xflag) memory->create(x,natoms,3,"molecule:x");
if (typeflag) memory->create(type,natoms,"molecule:type");
if (qflag) memory->create(q,natoms,"molecule:q");
if (radiusflag) memory->create(radius,natoms,"molecule:radius");
if (rmassflag) memory->create(rmass,natoms,"molecule:rmass");
// always allocate num_bond,num_angle,etc and nspecial even if not in file
// initialize to 0 even if not in molecule file
// this is so methods that use these arrays don't have to check they exist
memory->create(num_bond,natoms,"molecule:num_bond");
for (int i = 0; i < natoms; i++) num_bond[i] = 0;
memory->create(num_angle,natoms,"molecule:num_angle");
for (int i = 0; i < natoms; i++) num_angle[i] = 0;
memory->create(num_dihedral,natoms,"molecule:num_dihedral");
for (int i = 0; i < natoms; i++) num_dihedral[i] = 0;
memory->create(num_improper,natoms,"molecule:num_improper");
for (int i = 0; i < natoms; i++) num_improper[i] = 0;
memory->create(nspecial,natoms,3,"molecule:nspecial");
for (int i = 0; i < natoms; i++)
nspecial[i][0] = nspecial[i][1] = nspecial[i][2] = 0;
if (bondflag) {
memory->create(bond_type,natoms,bond_per_atom,
"molecule:bond_type");
memory->create(bond_atom,natoms,bond_per_atom,
"molecule:bond_atom");
}
if (angleflag) {
memory->create(angle_type,natoms,angle_per_atom,
"molecule:angle_type");
memory->create(angle_atom1,natoms,angle_per_atom,
"molecule:angle_atom1");
memory->create(angle_atom2,natoms,angle_per_atom,
"molecule:angle_atom2");
memory->create(angle_atom3,natoms,angle_per_atom,
"molecule:angle_atom3");
}
if (dihedralflag) {
memory->create(dihedral_type,natoms,dihedral_per_atom,
"molecule:dihedral_type");
memory->create(dihedral_atom1,natoms,dihedral_per_atom,
"molecule:dihedral_atom1");
memory->create(dihedral_atom2,natoms,dihedral_per_atom,
"molecule:dihedral_atom2");
memory->create(dihedral_atom3,natoms,dihedral_per_atom,
"molecule:dihedral_atom3");
memory->create(dihedral_atom4,natoms,dihedral_per_atom,
"molecule:dihedral_atom4");
}
if (improperflag) {
memory->create(improper_type,natoms,improper_per_atom,
"molecule:improper_type");
memory->create(improper_atom1,natoms,improper_per_atom,
"molecule:improper_atom1");
memory->create(improper_atom2,natoms,improper_per_atom,
"molecule:improper_atom2");
memory->create(improper_atom3,natoms,improper_per_atom,
"molecule:improper_atom3");
memory->create(improper_atom4,natoms,improper_per_atom,
"molecule:improper_atom4");
}
if (specialflag)
memory->create(special,natoms,maxspecial,"molecule:special");
if (shakeflag) {
memory->create(shake_flag,natoms,"molecule:shake_flag");
memory->create(shake_atom,natoms,4,"molecule:shake_flag");
memory->create(shake_type,natoms,3,"molecule:shake_flag");
}
}
/* ----------------------------------------------------------------------
deallocate all data structures
------------------------------------------------------------------------- */
void Molecule::deallocate()
{
memory->destroy(x);
memory->destroy(type);
memory->destroy(q);
memory->destroy(radius);
memory->destroy(rmass);
memory->destroy(num_bond);
memory->destroy(bond_type);
memory->destroy(bond_atom);
memory->destroy(num_angle);
memory->destroy(angle_type);
memory->destroy(angle_atom1);
memory->destroy(angle_atom2);
memory->destroy(angle_atom3);
memory->destroy(num_dihedral);
memory->destroy(dihedral_type);
memory->destroy(dihedral_atom1);
memory->destroy(dihedral_atom2);
memory->destroy(dihedral_atom3);
memory->destroy(dihedral_atom4);
memory->destroy(num_improper);
memory->destroy(improper_type);
memory->destroy(improper_atom1);
memory->destroy(improper_atom2);
memory->destroy(improper_atom3);
memory->destroy(improper_atom4);
memory->destroy(nspecial);
memory->destroy(special);
memory->destroy(shake_flag);
memory->destroy(shake_atom);
memory->destroy(shake_type);
memory->destroy(dx);
memory->destroy(dxcom);
memory->destroy(dxbody);
}
/* ----------------------------------------------------------------------
open molecule file
------------------------------------------------------------------------- */
void Molecule::open(char *file)
{
fp = fopen(file,"r");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open molecule file %s",file);
error->one(FLERR,str);
}
}
/* ----------------------------------------------------------------------
read and bcast a line
------------------------------------------------------------------------- */
void Molecule::readline(char *line)
{
int n;
if (me == 0) {
if (fgets(line,MAXLINE,fp) == NULL) n = 0;
else n = strlen(line) + 1;
}
MPI_Bcast(&n,1,MPI_INT,0,world);
if (n == 0) error->all(FLERR,"Unexpected end of molecule file");
MPI_Bcast(line,n,MPI_CHAR,0,world);
}
/* ----------------------------------------------------------------------
extract keyword from line
flag = 0, read and bcast line
flag = 1, line has already been read
------------------------------------------------------------------------- */
void Molecule::parse_keyword(int flag, char *line, char *keyword)
{
if (flag) {
// read upto non-blank line plus 1 following line
// eof is set to 1 if any read hits end-of-file
int eof = 0;
if (me == 0) {
if (fgets(line,MAXLINE,fp) == NULL) eof = 1;
while (eof == 0 && strspn(line," \t\n\r") == strlen(line)) {
if (fgets(line,MAXLINE,fp) == NULL) eof = 1;
}
if (fgets(keyword,MAXLINE,fp) == NULL) eof = 1;
}
// if eof, set keyword empty and return
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) {
keyword[0] = '\0';
return;
}
// bcast keyword line to all procs
int n;
if (me == 0) n = strlen(line) + 1;
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
}
// copy non-whitespace portion of line into keyword
int start = strspn(line," \t\n\r");
int stop = strlen(line) - 1;
while (line[stop] == ' ' || line[stop] == '\t'
|| line[stop] == '\n' || line[stop] == '\r') stop--;
line[stop+1] = '\0';
strcpy(keyword,&line[start]);
}
/* ----------------------------------------------------------------------
skip N lines of file
------------------------------------------------------------------------- */
void Molecule::skip_lines(int n, char *line)
{
for (int i = 0; i < n; i++) readline(line);
}
/* ----------------------------------------------------------------------
parse line into words separated by whitespace
return # of words
max = max pointers storable in words
------------------------------------------------------------------------- */
int Molecule::parse(char *line, char **words, int max)
{
char *ptr;
int nwords = 0;
words[nwords++] = strtok(line," \t\n\r\f");
while ((ptr = strtok(NULL," \t\n\r\f"))) {
if (nwords < max) words[nwords] = ptr;
nwords++;
}
return nwords;
}
/* ----------------------------------------------------------------------
proc 0 prints molecule params
------------------------------------------------------------------------- */
/*
void Molecule::print()
{
printf("MOLECULE %s\n",id);
printf(" %d natoms\n",natoms);
if (nbonds) printf(" %d nbonds\n",nbonds);
if (nangles) printf(" %d nangles\n",nangles);
if (ndihedrals) printf(" %d ndihedrals\n",ndihedrals);
if (nimpropers) printf(" %d nimpropers\n",nimpropers);
if (xflag) {
printf( "Coords:\n");
for (int i = 0; i < natoms; i++)
printf(" %d %g %g %g\n",i+1,x[i][0],x[i][1],x[i][2]);
}
if (typeflag) {
printf( "Types:\n");
for (int i = 0; i < natoms; i++)
printf(" %d %d\n",i+1,type[i]);
}
if (qflag) {
printf( "Charges:\n");
for (int i = 0; i < natoms; i++)
printf(" %d %g\n",i+1,q[i]);
}
if (radiusflag) {
printf( "Radii:\n");
for (int i = 0; i < natoms; i++)
printf(" %d %g\n",i+1,radius[i]);
}
if (rmassflag) {
printf( "Masses:\n");
for (int i = 0; i < natoms; i++)
printf(" %d %g\n",i+1,rmass[i]);
}
if (bondflag) {
printf( "Bonds:\n");
for (int i = 0; i < natoms; i++) {
printf(" %d %d\n",i+1,num_bond[i]);
for (int j = 0; j < num_bond[i]; j++)
printf(" %d %d %d %d\n",j+1,bond_type[i][j],i+1,bond_atom[i][j]);
}
}
if (angleflag) {
printf( "Angles:\n");
for (int i = 0; i < natoms; i++) {
printf(" %d %d\n",i+1,num_angle[i]);
for (int j = 0; j < num_angle[i]; j++)
printf(" %d %d %d %d %d\n",
j+1,angle_type[i][j],
angle_atom1[i][j],angle_atom2[i][j],angle_atom3[i][j]);
}
}
if (dihedralflag) {
printf( "Dihedrals:\n");
for (int i = 0; i < natoms; i++) {
printf(" %d %d\n",i+1,num_dihedral[i]);
for (int j = 0; j < num_dihedral[i]; j++)
printf(" %d %d %d %d %d %d\n",
j+1,dihedral_type[i][j],
dihedral_atom1[i][j],dihedral_atom2[i][j],
dihedral_atom3[i][j],dihedral_atom4[i][j]);
}
}
if (improperflag) {
printf( "Impropers:\n");
for (int i = 0; i < natoms; i++) {
printf(" %d %d\n",i+1,num_improper[i]);
for (int j = 0; j < num_improper[i]; j++)
printf(" %d %d %d %d %d %d\n",
j+1,improper_type[i][j],
improper_atom1[i][j],improper_atom2[i][j],
improper_atom3[i][j],improper_atom4[i][j]);
}
}
if (specialflag) {
printf( "Special neighs:\n");
for (int i = 0; i < natoms; i++) {
printf(" %d %d %d %d\n",i+1,
nspecial[i][0],nspecial[i][1]-nspecial[i][0],
nspecial[i][2]-nspecial[i][1]);
printf(" ");
for (int j = 0; j < nspecial[i][2]; j++)
printf(" %d",special[i][j]);
printf("\n");
}
}
}
*/
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