Commit d4291435 authored by jrgissing's avatar jrgissing
Browse files

bond/react: Arrhenius constraint

parent 5d475088

doc/src/Eqs/fix_bond_react.jpg

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+2.37 KiB
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doc/src/Eqs/fix_bond_react.tex

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\documentstyle[12pt]{article}

\pagestyle{empty}

\begin{document}



\begin{eqnarray*}

   k = AT^{n}e^{\frac{-E_{a}}{k_{B}T}}

\end{eqnarray*}                           



\end{document}

doc/src/fix_bond_react.txt

+22 −1
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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 are two types of constraints available, as discussed below.

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



A sample map file is given below:
@@ -320,6 +320,27 @@ 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 'arrhenius' imposes an additional reaction

probability according to the temperature-dependent Arrhenius equation:



:c,image(Eqs/fix_bond_react.jpg)



The Arrhenius constraint has the following syntax:



arrhenius {A} {n} {E_a} {seed} :pre



where 'arrhenius' is the required keyword, {A} is the pre-exponential

factor, {n} is the exponent of the temperature dependence, {E_a} is

the activation energy ("units"_units.html of energy), and {seed} is a

random number seed. The temperature is defined as the instantaneous

temperature averaged over all atoms in the reaction site, and is

calculated in the same manner as for example

"compute_temp_chunk"_compute_temp_chunk.html. Currently, there are no

options for additional temperature averaging or velocity-biased

temperature calculations. A uniform random number between 0 and 1 is

generated using {seed}; if this number is less than the result of the

Arrhenius equation above, the reaction is permitted occur.



Once a reaction site has been successfully identified, data structures

within LAMMPS that store bond topology are updated to reflect the

post-reacted molecule template. All force fields with fixed bonds,

src/USER-MISC/fix_bond_react.cpp

+64 −3
Original line number Diff line number Diff line
@@ -71,7 +71,7 @@ static const char cite_fix_bond_react[] = 
enum{ACCEPT,REJECT,PROCEED,CONTINUE,GUESSFAIL,RESTORE};



// types of available reaction constraints

enum{DISTANCE,ANGLE};

enum{DISTANCE,ANGLE,ARRHENIUS};



/* ---------------------------------------------------------------------- */
@@ -100,6 +100,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : 
  extvector = 0;

  rxnID = 0;

  nconstraints = 0;

  narrhenius = 0;

  status = PROCEED;



  nxspecial = NULL;
@@ -322,6 +323,16 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : 
    find_landlocked_atoms(i);

  }



  // initialize Marsaglia RNG with processor-unique seed (Arrhenius prob)



  rrhandom = new class RanMars*[narrhenius];

  int tmp = 0;

  for (int i = 0; i < nconstraints; i++) {

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

      rrhandom[tmp++] = new RanMars(lmp,(int) constraints[i][6] + me);

    }

  }



  for (int i = 0; i < nreacts; i++) {

    delete [] files[i];

  }
@@ -348,7 +359,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : 
    }

  }



  // initialize Marsaglia RNG with processor-unique seed

  // initialize Marsaglia RNG with processor-unique seed ('prob' keyword)



  random = new class RanMars*[nreacts];

  for (int i = 0; i < nreacts; i++) {
@@ -1640,7 +1651,7 @@ int FixBondReact::check_constraints() 
  tagint atom1,atom2,atom3;

  double delx,dely,delz,rsq;

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

  double rsq1,rsq2,r1,r2,c;

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



  double **x = atom->x;
@@ -1680,12 +1691,54 @@ 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] == ARRHENIUS) {

        t = get_temperature();

        prrhob = constraints[i][3]*pow(t,constraints[i][4])*

               exp(-constraints[i][5]/(force->boltz*t));

        if (prrhob < rrhandom[(int) constraints[i][2]]->uniform()) return 0;

      }

    }

  }

  return 1;

}



/* ----------------------------------------------------------------------

compute local temperature: average over all atoms in reaction template

------------------------------------------------------------------------- */



double FixBondReact::get_temperature()

{

  int i,ilocal;

  double adof = domain->dimension;



  double **v = atom->v;

  double *mass = atom->mass;

  double *rmass = atom->rmass;

  int *type = atom->type;



  double t = 0.0;



  if (rmass) {

    for (i = 0; i < onemol->natoms; i++) {

      ilocal = atom->map(glove[i][1]);

      t += (v[ilocal][0]*v[ilocal][0] + v[ilocal][1]*v[ilocal][1] +

        v[ilocal][2]*v[ilocal][2]) * rmass[ilocal];

    }

  } else {

    for (i = 0; i < onemol->natoms; i++) {

      ilocal = atom->map(glove[i][1]);

      t += (v[ilocal][0]*v[ilocal][0] + v[ilocal][1]*v[ilocal][1] +

        v[ilocal][2]*v[ilocal][2]) * mass[type[ilocal]];

    }

  }



  // final temperature

  double dof = adof*onemol->natoms;

  double tfactor = force->mvv2e / (dof * force->boltz);

  t *= tfactor;

  return t;

}



/* ----------------------------------------------------------------------

  Get xspecials for current molecule templates

------------------------------------------------------------------------- */
@@ -2947,6 +3000,14 @@ 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,"arrhenius") == 0) {

      constraints[nconstraints][1] = ARRHENIUS;

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

      sscanf(line,"%*s %lg %lg %lg %lg",&tmp[0],&tmp[1],&tmp[2],&tmp[3]);

      constraints[nconstraints][3] = tmp[0];

      constraints[nconstraints][4] = tmp[1];

      constraints[nconstraints][5] = tmp[2];

      constraints[nconstraints][6] = tmp[3];

    } else

      error->one(FLERR,"Bond/react: Illegal constraint type in 'Constraints' section of map file");

    nconstraints++;

src/USER-MISC/fix_bond_react.h

+4 −1
Original line number Diff line number Diff line
@@ -65,6 +65,7 @@ class FixBondReact : public Fix { 
  int *stabilize_steps_flag;

  int *update_edges_flag;

  int nconstraints;

  int narrhenius;

  double **constraints;

  int status;

  int *groupbits;
@@ -88,7 +89,8 @@ class FixBondReact : public Fix { 
  Fix *fix2;              // properties/atom used to indicate 1) relaxing atoms

                          //                                  2) to which 'react' atom belongs

  Fix *fix3;              // property/atom used for system-wide thermostat

  class RanMars **random;

  class RanMars **random; // random number for 'prob' keyword

  class RanMars **rrhandom; // random number for Arrhenius constraint

  class NeighList *list;



  int *reacted_mol,*unreacted_mol;
@@ -156,6 +158,7 @@ class FixBondReact : public Fix { 
  void inner_crosscheck_loop();

  void ring_check();

  int check_constraints();

  double get_temperature();



  void open(char *);

  void readline(char *);

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