Commit a35dc180 authored by jrgissing's avatar jrgissing
Browse files

bond/react: dihedral reaction constraint

parent d897949f

doc/src/fix_bond_react.rst

+19 −1
Original line number Diff line number Diff line
@@ -294,7 +294,7 @@ either 'none' or 'charges.' Further details are provided in the 
discussion of the 'update\_edges' keyword. The fifth optional section

begins with the keyword 'Constraints' and lists additional criteria

that must be satisfied in order for the reaction to occur. Currently,

there are three types of constraints available, as discussed below.

there are four types of constraints available, as discussed below.



A sample map file is given below:
@@ -370,6 +370,24 @@ the central atom). Angles must be specified in degrees. This 
constraint can be used to enforce a certain orientation between

reacting molecules.



The constraint of type 'dihedral' has the following syntax:





.. parsed-literal::



   dihedral *ID1* *ID2* *ID3* *ID4* *amin* *amax* *amin2* *amax2*



where 'dihedral' is the required keyword, and *ID1*\ , *ID2*\ , *ID3*

and *ID4* are pre-reaction atom IDs. Dihedral angles are calculated in

the interval (-180,180]. Refer to the :doc:`dihedral style <dihedral_style>`

documentation for further details on convention. If *amin* is less

than *amax*, these four atoms must form a dihedral angle greater than

*amin* **and** less than *amax* for the reaction to occur. If *amin*

is greater than *amax*, these four atoms must form a dihedral angle

greater than *amin* **or** less than *amax* for the reaction to occur.

Angles must be specified in degrees. Optionally, a second range of

permissible angles *amin2*-*amax2* can be specified.



The constraint of type 'arrhenius' imposes an additional reaction

probability according to the temperature-dependent Arrhenius equation:

src/USER-REACTION/fix_bond_react.cpp

+85 −3
Original line number Diff line number Diff line
@@ -60,7 +60,7 @@ 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 7 // max # of arguments for any type of constraint + rxnID

#define MAXCONARGS 10 // max # of arguments for any type of constraint + rxnID



// various statuses of superimpose algorithm:

// ACCEPT: site successfully matched to pre-reacted template
@@ -72,7 +72,7 @@ static const char cite_fix_bond_react[] = 
enum{ACCEPT,REJECT,PROCEED,CONTINUE,GUESSFAIL,RESTORE};



// types of available reaction constraints

enum{DISTANCE,ANGLE,ARRHENIUS};

enum{DISTANCE,ANGLE,DIHEDRAL,ARRHENIUS};



/* ---------------------------------------------------------------------- */
@@ -1654,10 +1654,15 @@ evaluate constraints: return 0 if any aren't satisfied 


int FixBondReact::check_constraints()

{

  tagint atom1,atom2,atom3;

  tagint atom1,atom2,atom3,atom4;

  double delx,dely,delz,rsq;

  double delx1,dely1,delz1,delx2,dely2,delz2;

  double rsq1,rsq2,r1,r2,c,t,prrhob;

  // for computation of dihedrals

  double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;

  double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,ra2inv,rb2inv,rabinv;

  double s,phi;

  int ANDgate;



  double **x = atom->x;
@@ -1699,6 +1704,69 @@ int FixBondReact::check_constraints() 
        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;

      } else if (constraints[i][1] == DIHEDRAL) {

        // phi calculation from dihedral style harmonic

        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]);

        atom4 = atom->map(glove[(int) constraints[i][5]-1][1]);



        vb1x = x[atom1][0] - x[atom2][0];

        vb1y = x[atom1][1] - x[atom2][1];

        vb1z = x[atom1][2] - x[atom2][2];

        domain->minimum_image(vb1x,vb1y,vb1z);



        vb2x = x[atom3][0] - x[atom2][0];

        vb2y = x[atom3][1] - x[atom2][1];

        vb2z = x[atom3][2] - x[atom2][2];

        domain->minimum_image(vb2x,vb2y,vb2z);



        vb2xm = -vb2x;

        vb2ym = -vb2y;

        vb2zm = -vb2z;

        domain->minimum_image(vb2xm,vb2ym,vb2zm);



        vb3x = x[atom4][0] - x[atom3][0];

        vb3y = x[atom4][1] - x[atom3][1];

        vb3z = x[atom4][2] - x[atom3][2];

        domain->minimum_image(vb3x,vb3y,vb3z);



        ax = vb1y*vb2zm - vb1z*vb2ym;

        ay = vb1z*vb2xm - vb1x*vb2zm;

        az = vb1x*vb2ym - vb1y*vb2xm;

        bx = vb3y*vb2zm - vb3z*vb2ym;

        by = vb3z*vb2xm - vb3x*vb2zm;

        bz = vb3x*vb2ym - vb3y*vb2xm;



        rasq = ax*ax + ay*ay + az*az;

        rbsq = bx*bx + by*by + bz*bz;

        rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;

        rg = sqrt(rgsq);



        ra2inv = rb2inv = 0.0;

        if (rasq > 0) ra2inv = 1.0/rasq;

        if (rbsq > 0) rb2inv = 1.0/rbsq;

        rabinv = sqrt(ra2inv*rb2inv);



        c = (ax*bx + ay*by + az*bz)*rabinv;

        s = rg*rabinv*(ax*vb3x + ay*vb3y + az*vb3z);



        if (c > 1.0) c = 1.0;

        if (c < -1.0) c = -1.0;

        phi = atan2(s,c);



        ANDgate = 0;

        if (constraints[i][6] < constraints[i][7]) {

          if (phi > constraints[i][6] && phi < constraints[i][7]) ANDgate = 1;

        } else {

          if (phi > constraints[i][6] || phi < constraints[i][7]) ANDgate = 1;

        }

        if (constraints[i][8] < constraints[i][9]) {

          if (phi > constraints[i][8] && phi < constraints[i][9]) ANDgate = 1;

        } else {

          if (phi > constraints[i][8] || phi < constraints[i][9]) ANDgate = 1;

        }

        if (ANDgate != 1) return 0;

      } else if (constraints[i][1] == ARRHENIUS) {

        t = get_temperature();

        prrhob = constraints[i][3]*pow(t,constraints[i][4])*
@@ -3110,6 +3178,20 @@ void FixBondReact::Constraints(char *line, int myrxn) 
      constraints[nconstraints][4] = tmp[2];

      constraints[nconstraints][5] = tmp[3]/180.0 * MY_PI;

      constraints[nconstraints][6] = tmp[4]/180.0 * MY_PI;

    } else if (strcmp(constraint_type,"dihedral") == 0) {

      constraints[nconstraints][1] = DIHEDRAL;

      tmp[6] = 181.0; // impossible range

      tmp[7] = 182.0;

      sscanf(line,"%*s %lg %lg %lg %lg %lg %lg %lg %lg",&tmp[0],&tmp[1],

                        &tmp[2],&tmp[3],&tmp[4],&tmp[5],&tmp[6],&tmp[7]);

      constraints[nconstraints][2] = tmp[0];

      constraints[nconstraints][3] = tmp[1];

      constraints[nconstraints][4] = tmp[2];

      constraints[nconstraints][5] = tmp[3];

      constraints[nconstraints][6] = tmp[4]/180.0 * MY_PI;

      constraints[nconstraints][7] = tmp[5]/180.0 * MY_PI;

      constraints[nconstraints][8] = tmp[6]/180.0 * MY_PI;

      constraints[nconstraints][9] = tmp[7]/180.0 * MY_PI;

    } else if (strcmp(constraint_type,"arrhenius") == 0) {

      constraints[nconstraints][1] = ARRHENIUS;

      constraints[nconstraints][2] = narrhenius++;

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