forked from lijiext/lammps
Merge pull request #1795 from jrgissing/bond/react-chiral_centers
Bond/react chiral centers
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Axel Kohlmeyer
GitHub
commit
402f5585ff
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@ -518,6 +518,16 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
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*Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted*
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Self-explanatory.
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*Bond/react: First neighbors of chiral atoms must be of mutually different types*
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Self-explanatory.
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*Bond/react: Chiral atoms must have exactly four first neighbors*
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Self-explanatory.
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*Bond/react: Molecule template 'Coords' section required for chiralIDs keyword*
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The coordinates of atoms in the pre-reacted template are used to determine
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chirality.
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*Bond/react special bond generation overflow*
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The number of special bonds per-atom created by a reaction exceeds the
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system setting. See the read\_data or create\_box command for how to
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@ -20,9 +20,9 @@ Syntax
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* the common keyword/values may be appended directly after 'bond/react'
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* this applies to all reaction specifications (below)
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* common\_keyword = *stabilization*
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.. parsed-literal::
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*stabilization* values = *no* or *yes* *group-ID* *xmax*
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*no* = no reaction site stabilization
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*yes* = perform reaction site stabilization
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@ -40,9 +40,9 @@ Syntax
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* map\_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates
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* zero or more individual keyword/value pairs may be appended to each react argument
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* individual\_keyword = *prob* or *max\_rxn* or *stabilize\_steps* or *update\_edges*
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.. parsed-literal::
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*prob* values = fraction seed
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fraction = initiate reaction with this probability if otherwise eligible
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seed = random number seed (positive integer)
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@ -253,7 +253,7 @@ A discussion of correctly handling this is also provided on the
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The map file is a text document with the following format:
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A map file has a header and a body. The header of map file the
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contains one mandatory keyword and four optional keywords. The
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contains one mandatory keyword and five optional keywords. The
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mandatory keyword is 'equivalences':
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@ -269,10 +269,11 @@ The optional keywords are 'edgeIDs', 'deleteIDs', 'customIDs' and
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N *edgeIDs* = # of edge atoms N in the pre-reacted molecule template
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N *deleteIDs* = # of atoms N that are specified for deletion
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N *chiralIDs* = # of specified chiral centers N
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N *customIDs* = # of atoms N that are specified for a custom update
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N *constraints* = # of specified reaction constraints N
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The body of the map file contains two mandatory sections and four
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The body of the map file contains two mandatory sections and five
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optional sections. The first mandatory section begins with the keyword
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'BondingIDs' and lists the atom IDs of the bonding atom pair in the
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pre-reacted molecule template. The second mandatory section begins
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@ -284,12 +285,14 @@ molecule template. The first optional section begins with the keyword
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'EdgeIDs' and lists the atom IDs of edge atoms in the pre-reacted
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molecule template. The second optional section begins with the keyword
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'DeleteIDs' and lists the atom IDs of pre-reaction template atoms to
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delete. The third optional section begins with the keyword 'Custom
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delete. The third optional section begins with the keyword 'ChiralIDs'
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lists the atom IDs of chiral atoms whose handedness should be
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enforced. The fourth optional section begins with the keyword 'Custom
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Edges' and allows for forcing the update of a specific atom's atomic
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charge. The first column is the ID of an atom near the edge of the
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pre-reacted molecule template, and the value of the second column is
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either 'none' or 'charges.' Further details are provided in the
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discussion of the 'update\_edges' keyword. The fourth optional section
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discussion of the 'update\_edges' keyword. The fifth optional section
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begins with the keyword 'Constraints' and lists additional criteria
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that must be satisfied in order for the reaction to occur. Currently,
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there are three types of constraints available, as discussed below.
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@ -332,6 +335,15 @@ A sample map file is given below:
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----------
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The handedness of atoms that are chiral centers can be enforced by
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listing their IDs in the ChiralIDs section. A chiral atom must be
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bonded to four atoms with mutually different atom types. This feature
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uses the coordinates and types of the involved atoms in the
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pre-reaction template to determine handedness. Three atoms bonded to
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the chiral center are arbitrarily chosen, to define an oriented plane,
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and the relative position of the fourth bonded atom determines the
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chiral center's handedness.
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Any number of additional constraints may be specified in the
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Constraints section of the map file. The constraint of type 'distance'
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has syntax as follows:
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@ -36,6 +36,7 @@ Contributing Author: Jacob Gissinger (jacob.gissinger@colorado.edu)
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#include "group.h"
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#include "citeme.h"
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#include "math_const.h"
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#include "math_extra.h"
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#include "memory.h"
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#include "error.h"
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@ -297,6 +298,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
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memory->create(landlocked_atoms,max_natoms,nreacts,"bond/react:landlocked_atoms");
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memory->create(custom_edges,max_natoms,nreacts,"bond/react:custom_edges");
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memory->create(delete_atoms,max_natoms,nreacts,"bond/react:delete_atoms");
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memory->create(chiral_atoms,max_natoms,6,nreacts,"bond/react:chiral_atoms");
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for (int j = 0; j < nreacts; j++)
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for (int i = 0; i < max_natoms; i++) {
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@ -304,6 +306,9 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
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if (update_edges_flag[j] == 1) custom_edges[i][j] = 1;
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else custom_edges[i][j] = 0;
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delete_atoms[i][j] = 0;
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for (int k = 0; k < 6; k++) {
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chiral_atoms[i][k][j] = 0;
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}
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}
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// read all map files afterward
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@ -430,6 +435,7 @@ FixBondReact::~FixBondReact()
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memory->destroy(landlocked_atoms);
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memory->destroy(custom_edges);
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memory->destroy(delete_atoms);
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memory->destroy(chiral_atoms);
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memory->destroy(nevery);
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memory->destroy(cutsq);
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@ -1675,6 +1681,7 @@ int FixBondReact::check_constraints()
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delx1 = x[atom1][0] - x[atom2][0];
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dely1 = x[atom1][1] - x[atom2][1];
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delz1 = x[atom1][2] - x[atom2][2];
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domain->minimum_image(delx1,dely1,delz1); // ghost location fix
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rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
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r1 = sqrt(rsq1);
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@ -1682,6 +1689,7 @@ int FixBondReact::check_constraints()
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delx2 = x[atom3][0] - x[atom2][0];
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dely2 = x[atom3][1] - x[atom2][1];
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delz2 = x[atom3][2] - x[atom2][2];
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domain->minimum_image(delx2,dely2,delz2); // ghost location fix
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rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
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r2 = sqrt(rsq2);
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@ -1699,6 +1707,30 @@ int FixBondReact::check_constraints()
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}
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}
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}
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// let's also check chirality within 'check_constraint'
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for (int i = 0; i < onemol->natoms; i++) {
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if (chiral_atoms[i][0][rxnID] == 1) {
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double my4coords[12];
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// already ensured, by transitive property, that chiral simulation atom has four neighs
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for (int j = 0; j < 4; j++) {
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atom1 = atom->map(glove[i][1]);
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// loop over known types involved in chiral center
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for (int jj = 0; jj < 4; jj++) {
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if (atom->type[atom->map(xspecial[atom1][j])] == chiral_atoms[i][jj+2][rxnID]) {
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atom2 = atom->map(xspecial[atom1][j]);
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atom2 = domain->closest_image(atom1,atom2);
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for (int k = 0; k < 3; k++) {
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my4coords[3*jj+k] = x[atom2][k];
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}
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break;
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}
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}
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}
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if (get_chirality(my4coords) != chiral_atoms[i][1][rxnID]) return 0;
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}
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}
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return 1;
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}
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@ -1739,6 +1771,33 @@ double FixBondReact::get_temperature()
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return t;
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}
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/* ----------------------------------------------------------------------
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return handedness (1 or -1) of a chiral center, given ordered set of coordinates
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------------------------------------------------------------------------- */
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int FixBondReact::get_chirality(double four_coords[12])
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{
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// define oriented plane with first three coordinates
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double vec1[3],vec2[3],vec3[3],vec4[3],mean3[3],dot;
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for (int i = 0; i < 3; i++) {
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vec1[i] = four_coords[i]-four_coords[i+3];
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vec2[i] = four_coords[i+3]-four_coords[i+6];
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}
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MathExtra::cross3(vec1,vec2,vec3);
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for (int i = 0; i < 3; i++) {
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mean3[i] = (four_coords[i] + four_coords[i+3] +
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four_coords[i+6])/3;
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vec4[i] = four_coords[i+9] - mean3[i];
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}
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dot = MathExtra::dot3(vec3,vec4);
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dot = dot/fabs(dot);
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return (int) dot;
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}
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/* ----------------------------------------------------------------------
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Get xspecials for current molecule templates
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------------------------------------------------------------------------- */
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@ -2867,6 +2926,7 @@ void FixBondReact::read(int myrxn)
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}
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else if (strstr(line,"customIDs")) sscanf(line,"%d",&ncustom);
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else if (strstr(line,"deleteIDs")) sscanf(line,"%d",&ndelete);
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else if (strstr(line,"chiralIDs")) sscanf(line,"%d",&nchiral);
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else if (strstr(line,"constraints")) {
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sscanf(line,"%d",&nconstr);
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memory->grow(constraints,nconstraints+nconstr,MAXCONARGS,"bond/react:constraints");
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@ -2898,6 +2958,8 @@ void FixBondReact::read(int myrxn)
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CustomEdges(line, myrxn);
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} else if (strcmp(keyword,"DeleteIDs") == 0) {
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DeleteAtoms(line, myrxn);
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} else if (strcmp(keyword,"ChiralIDs") == 0) {
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ChiralCenters(line, myrxn);
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} else if (strcmp(keyword,"Constraints") == 0) {
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Constraints(line, myrxn);
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} else error->one(FLERR,"Bond/react: Unknown section in map file");
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@ -2975,6 +3037,37 @@ void FixBondReact::DeleteAtoms(char *line, int myrxn)
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}
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}
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void FixBondReact::ChiralCenters(char *line, int myrxn)
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{
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int tmp;
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for (int i = 0; i < nchiral; i++) {
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readline(line);
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sscanf(line,"%d",&tmp);
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chiral_atoms[tmp-1][0][myrxn] = 1;
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if (onemol->xflag == 0)
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error->one(FLERR,"Bond/react: Molecule template 'Coords' section required for chiralIDs keyword");
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if ((int) onemol_nxspecial[tmp-1][0] != 4)
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error->one(FLERR,"Bond/react: Chiral atoms must have exactly four first neighbors");
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for (int j = 0; j < 4; j++) {
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for (int k = j+1; k < 4; k++) {
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if (onemol->type[onemol_xspecial[tmp-1][j]-1] ==
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onemol->type[onemol_xspecial[tmp-1][k]-1])
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error->one(FLERR,"Bond/react: First neighbors of chiral atoms must be of mutually different types");
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}
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}
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// record order of atom types, and coords
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double my4coords[12];
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for (int j = 0; j < 4; j++) {
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chiral_atoms[tmp-1][j+2][myrxn] = onemol->type[onemol_xspecial[tmp-1][j]-1];
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for (int k = 0; k < 3; k++) {
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my4coords[3*j+k] = onemol->x[onemol_xspecial[tmp-1][j]-1][k];
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}
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}
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// get orientation
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chiral_atoms[tmp-1][1][myrxn] = get_chirality(my4coords);
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}
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}
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void FixBondReact::Constraints(char *line, int myrxn)
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{
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double tmp[MAXCONARGS];
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@ -110,7 +110,7 @@ class FixBondReact : public Fix {
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int *ibonding,*jbonding;
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int *closeneigh; // indicates if bonding atoms of a rxn are 1-2, 1-3, or 1-4 neighbors
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int nedge,nequivalent,ncustom,ndelete,nconstr; // # edge, equivalent, custom atoms in mapping file
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int nedge,nequivalent,ncustom,ndelete,nchiral,nconstr; // # edge, equivalent, custom atoms in mapping file
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int attempted_rxn; // there was an attempt!
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int *local_rxn_count;
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int *ghostly_rxn_count;
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@ -126,6 +126,7 @@ class FixBondReact : public Fix {
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int **landlocked_atoms; // all atoms at least three bonds away from edge atoms
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int **custom_edges; // atoms in molecule templates with incorrect valences
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int **delete_atoms; // atoms in pre-reacted templates to delete
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int ***chiral_atoms; // pre-react chiral atoms. 1) flag 2) orientation 3-4) ordered atom types
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int **nxspecial,**onemol_nxspecial,**twomol_nxspecial; // full number of 1-4 neighbors
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tagint **xspecial,**onemol_xspecial,**twomol_xspecial; // full 1-4 neighbor list
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@ -149,6 +150,7 @@ class FixBondReact : public Fix {
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void Equivalences(char *,int);
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void CustomEdges(char *,int);
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void DeleteAtoms(char *,int);
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void ChiralCenters(char *,int);
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void Constraints(char *,int);
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void make_a_guess ();
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@ -159,6 +161,7 @@ class FixBondReact : public Fix {
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void ring_check();
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int check_constraints();
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double get_temperature();
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int get_chirality(double[12]); // get handedness given an ordered set of coordinates
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void open(char *);
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void readline(char *);
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@ -249,6 +252,18 @@ E: Bond/react: A deleted atom cannot remain bonded to an atom that is not delete
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Self-explanatory.
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E: Bond/react: First neighbors of chiral atoms must be of mutually different types
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Self-explanatory.
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E: Bond/react: Chiral atoms must have exactly four first neighbors
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Self-explanatory.
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E: Bond/react: Molecule template 'Coords' section required for chiralIDs keyword
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The coordinates of atoms in the pre-reacted template are used to determine chirality.
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E: Bond/react special bond generation overflow
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The number of special bonds per-atom created by a reaction exceeds the
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