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Merge pull request #1697 from jrgissing/bond/react-angle-constraints 

Bond/react: angle constraints
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Axel Kohlmeyer 2019-10-04 09:54:23 +02:00 committed by GitHub
parent aa2b885783 23040a98f8
commit ed87faec17
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3 changed files with 104 additions and 29 deletions
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17
doc/src/fix_bond_react.txt
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@ -266,7 +266,7 @@ either 'none' or 'charges.' Further details are provided in the
discussion of the 'update_edges' keyword. The fourth optional section
begins with the keyword 'Constraints' and lists additional criteria
that must be satisfied in order for the reaction to occur. Currently,
there is one type of constraint available, as discussed below.
there are two types of constraints available, as discussed below.
A sample map file is given below:
@ -300,14 +300,23 @@ Equivalences :pre
:line
Any number of additional constraints may be specified in the
Constraints section of the map file. Currently there is one type of
additional constraint, of type 'distance', whose syntax is as follows:
Constraints section of the map file. The constraint of type 'distance'
has syntax as follows:
distance {ID1} {ID2} {rmin} {rmax} :pre
where 'distance' is the required keyword, {ID1} and {ID2} are
pre-reaction atom IDs, and these two atoms must be separated by a
distance between {rmin} and {rmax} for the reaction to occur. This
distance between {rmin} and {rmax} for the reaction to occur.
The constraint of type 'angle' has the following syntax:
angle {ID1} {ID2} {ID3} {amin} {amax} :pre
where 'angle' is the required keyword, {ID1}, {ID2} and {ID3} are
pre-reaction atom IDs, and these three atoms must form an angle
between {amin} and {amax} for the reaction to occur (where {ID2} is
the central atom). Angles must be specified in degrees. This
constraint can be used to enforce a certain orientation between
reacting molecules.

112
src/USER-MISC/fix_bond_react.cpp
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@ -35,6 +35,7 @@ Contributing Author: Jacob Gissinger (jacob.gissinger@colorado.edu)
#include "molecule.h"
#include "group.h"
#include "citeme.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
@ -42,6 +43,7 @@ Contributing Author: Jacob Gissinger (jacob.gissinger@colorado.edu)
using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
static const char cite_fix_bond_react[] =
"fix bond/react:\n\n"
@ -57,7 +59,7 @@ static const char cite_fix_bond_react[] =
#define BIG 1.0e20
#define DELTA 16
#define MAXGUESS 20 // max # of guesses allowed by superimpose algorithm
#define MAXCONARGS 5 // max # of arguments for any type of constraint
#define MAXCONARGS 7 // max # of arguments for any type of constraint + rxnID
// various statuses of superimpose algorithm:
// ACCEPT: site successfully matched to pre-reacted template
@ -68,6 +70,9 @@ static const char cite_fix_bond_react[] =
// RESTORE: restore mode, load most recent restore point
enum{ACCEPT,REJECT,PROCEED,CONTINUE,GUESSFAIL,RESTORE};
// types of available reaction constraints
enum{DISTANCE,ANGLE};
/* ---------------------------------------------------------------------- */
FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
@ -94,6 +99,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
global_freq = 1;
extvector = 0;
rxnID = 0;
nconstraints = 0;
status = PROCEED;
nxspecial = NULL;
@ -169,8 +175,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
memory->create(limit_duration,nreacts,"bond/react:limit_duration");
memory->create(stabilize_steps_flag,nreacts,"bond/react:stabilize_steps_flag");
memory->create(update_edges_flag,nreacts,"bond/react:update_edges_flag");
memory->create(nconstraints,nreacts,"bond/react:nconstraints");
memory->create(constraints,nreacts,MAXCONARGS,"bond/react:constraints");
memory->create(constraints,1,MAXCONARGS,"bond/react:constraints");
memory->create(iatomtype,nreacts,"bond/react:iatomtype");
memory->create(jatomtype,nreacts,"bond/react:jatomtype");
memory->create(ibonding,nreacts,"bond/react:ibonding");
@ -188,7 +193,6 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
max_rxn[i] = INT_MAX;
stabilize_steps_flag[i] = 0;
update_edges_flag[i] = 0;
nconstraints[i] = 0;
// set default limit duration to 60 timesteps
limit_duration[i] = 60;
reaction_count[i] = 0;
@ -1138,6 +1142,22 @@ void FixBondReact::superimpose_algorithm()
glove[myjbonding-1][1] = created[lcl_inst][1][rxnID];
glove_counter++;
// special case, only two atoms in reaction templates
// then: bonding onemol_nxspecials guaranteed to be equal, and either 0 or 1
if (glove_counter == onemol->natoms) {
tagint local_atom1 = atom->map(glove[myibonding-1][1]);
tagint local_atom2 = atom->map(glove[myjbonding-1][1]);
if ( (nxspecial[local_atom1][0] == onemol_nxspecial[myibonding-1][0] &&
nxspecial[local_atom2][0] == nxspecial[local_atom1][0]) &&
(nxspecial[local_atom1][0] == 0 ||
xspecial[local_atom1][0] == atom->tag[local_atom2]) &&
check_constraints() ) {
status = ACCEPT;
glove_ghostcheck();
} else
status = REJECT;
}
avail_guesses = 0;
for (int i = 0; i < max_natoms; i++)
@ -1617,21 +1637,50 @@ evaluate constraints: return 0 if any aren't satisfied
int FixBondReact::check_constraints()
{
tagint atom1,atom2;
tagint atom1,atom2,atom3;
double delx,dely,delz,rsq;
double delx1,dely1,delz1,delx2,dely2,delz2;
double rsq1,rsq2,r1,r2,c;
double **x = atom->x;
for (int i = 0; i < nconstraints[rxnID]; i++) {
if (constraints[rxnID][0] == 0) { // 'distance' type
atom1 = atom->map(glove[(int) constraints[rxnID][1]-1][1]);
atom2 = atom->map(glove[(int) constraints[rxnID][2]-1][1]);
delx = x[atom1][0] - x[atom2][0];
dely = x[atom1][1] - x[atom2][1];
delz = x[atom1][2] - x[atom2][2];
domain->minimum_image(delx,dely,delz); // ghost location fix
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < constraints[rxnID][3] || rsq > constraints[rxnID][4]) return 0;
for (int i = 0; i < nconstraints; i++) {
if (constraints[i][0] == rxnID) {
if (constraints[i][1] == DISTANCE) {
atom1 = atom->map(glove[(int) constraints[i][2]-1][1]);
atom2 = atom->map(glove[(int) constraints[i][3]-1][1]);
delx = x[atom1][0] - x[atom2][0];
dely = x[atom1][1] - x[atom2][1];
delz = x[atom1][2] - x[atom2][2];
domain->minimum_image(delx,dely,delz); // ghost location fix
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < constraints[i][4] || rsq > constraints[i][5]) return 0;
} else if (constraints[i][1] == ANGLE) {
atom1 = atom->map(glove[(int) constraints[i][2]-1][1]);
atom2 = atom->map(glove[(int) constraints[i][3]-1][1]);
atom3 = atom->map(glove[(int) constraints[i][4]-1][1]);
// 1st bond
delx1 = x[atom1][0] - x[atom2][0];
dely1 = x[atom1][1] - x[atom2][1];
delz1 = x[atom1][2] - x[atom2][2];
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
r1 = sqrt(rsq1);
// 2nd bond
delx2 = x[atom3][0] - x[atom2][0];
dely2 = x[atom3][1] - x[atom2][1];
delz2 = x[atom3][2] - x[atom2][2];
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
r2 = sqrt(rsq2);
// angle (cos and sin)
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
if (acos(c) < constraints[i][5] || acos(c) > constraints[i][6]) return 0;
}
}
}
return 1;
@ -2757,13 +2806,20 @@ void FixBondReact::read(int myrxn)
if (strspn(line," \t\n\r") == strlen(line)) continue;
if (strstr(line,"edgeIDs")) sscanf(line,"%d",&nedge);
else if (strstr(line,"equivalences")) sscanf(line,"%d",&nequivalent);
else if (strstr(line,"equivalences")) {
sscanf(line,"%d",&nequivalent);
if (nequivalent != onemol->natoms)
error->one(FLERR,"Bond/react: Number of equivalences in map file must "
"equal number of atoms in reaction templates");
}
else if (strstr(line,"customIDs")) sscanf(line,"%d",&ncustom);
else if (strstr(line,"deleteIDs")) sscanf(line,"%d",&ndelete);
else if (strstr(line,"constraints")) sscanf(line,"%d",&nconstraints[myrxn]);
else if (strstr(line,"constraints")) sscanf(line,"%d",&nconstr);
else break;
}
memory->grow(constraints,nconstraints+nconstr,MAXCONARGS,"bond/react:constraints");
//count = NULL;
// grab keyword and skip next line
@ -2874,18 +2930,28 @@ void FixBondReact::Constraints(char *line, int myrxn)
double tmp[MAXCONARGS];
int n = strlen("distance") + 1;
char *constraint_type = new char[n];
for (int i = 0; i < nconstraints[myrxn]; i++) {
for (int i = 0; i < nconstr; i++) {
readline(line);
sscanf(line,"%s",constraint_type);
constraints[nconstraints][0] = myrxn;
if (strcmp(constraint_type,"distance") == 0) {
constraints[myrxn][0] = 0; // 0 = 'distance' ...maybe use another enum eventually
constraints[nconstraints][1] = DISTANCE;
sscanf(line,"%*s %lg %lg %lg %lg",&tmp[0],&tmp[1],&tmp[2],&tmp[3]);
constraints[myrxn][1] = tmp[0];
constraints[myrxn][2] = tmp[1];
constraints[myrxn][3] = tmp[2]*tmp[2]; // using square of distance
constraints[myrxn][4] = tmp[3]*tmp[3];
constraints[nconstraints][2] = tmp[0];
constraints[nconstraints][3] = tmp[1];
constraints[nconstraints][4] = tmp[2]*tmp[2]; // using square of distance
constraints[nconstraints][5] = tmp[3]*tmp[3];
} else if (strcmp(constraint_type,"angle") == 0) {
constraints[nconstraints][1] = ANGLE;
sscanf(line,"%*s %lg %lg %lg %lg %lg",&tmp[0],&tmp[1],&tmp[2],&tmp[3],&tmp[4]);
constraints[nconstraints][2] = tmp[0];
constraints[nconstraints][3] = tmp[1];
constraints[nconstraints][4] = tmp[2];
constraints[nconstraints][5] = tmp[3]/180.0 * MY_PI;
constraints[nconstraints][6] = tmp[4]/180.0 * MY_PI;
} else
error->one(FLERR,"Bond/react: Illegal constraint type in 'Constraints' section of map file");
nconstraints++;
}
delete [] constraint_type;
}

4
src/USER-MISC/fix_bond_react.h
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@ -64,7 +64,7 @@ class FixBondReact : public Fix {
int custom_exclude_flag;
int *stabilize_steps_flag;
int *update_edges_flag;
int *nconstraints;
int nconstraints;
double **constraints;
int status;
int *groupbits;
@ -108,7 +108,7 @@ class FixBondReact : public Fix {
int *ibonding,*jbonding;
int *closeneigh; // indicates if bonding atoms of a rxn are 1-2, 1-3, or 1-4 neighbors
int nedge,nequivalent,ncustom,ndelete; // number of edge, equivalent, custom atoms in mapping file
int nedge,nequivalent,ncustom,ndelete,nconstr; // # edge, equivalent, custom atoms in mapping file
int attempted_rxn; // there was an attempt!
int *local_rxn_count;
int *ghostly_rxn_count;