Commit d9d33ac7 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

add ability to set multiplicity for dihedrals with fix restrain 

this introduces an optional keyword, so backward compatibility is preserved.
this closes #884
parent d51745fd

doc/src/fix_restrain.txt

+9 −5
Original line number Diff line number Diff line
@@ -24,10 +24,12 @@ keyword = {bond} or {angle} or {dihedral} :l 
    atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom

    Kstart,Kstop = restraint coefficients at start/end of run (energy units)

    theta0 = equilibrium angle theta (degrees)

  {dihedral} args = atom1 atom2 atom3 atom4 Kstart Kstop phi0

  {dihedral} args = atom1 atom2 atom3 atom4 Kstart Kstop phi0 keyword/value

    atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order

    Kstart,Kstop = restraint coefficients at start/end of run (energy units)

    phi0 = equilibrium dihedral angle phi (degrees) :pre

    phi0 = equilibrium dihedral angle phi (degrees)

    keyword/value = optional keyword value pairs. supported keyword/value pairs:

      {mult} n = dihedral multiplicity n (integer >= 0, default = 1) :pre

:ule



[Examples:]
@@ -155,11 +157,13 @@ associated with the restraint is 
with the following coefficients:



K (energy)

n = 1

n (multiplicity, >= 0)

d (degrees) = phi0 + 180 :ul



K and phi0 are specified with the fix.  Note that the value of n is

hard-wired to 1.  Also note that the energy will be a minimum when the

K and phi0 are specified with the fix.  Note that the value of the

dihedral multiplicity {n} is set by default to 1. You can use the

optional {mult} keyword to set it to a different positive integer.

Also note that the energy will be a minimum when the

current dihedral angle phi is equal to phi0.



:line

src/fix_restrain.cpp

+14 −5
Original line number Diff line number Diff line
@@ -45,7 +45,7 @@ enum{BOND,ANGLE,DIHEDRAL}; 


FixRestrain::FixRestrain(LAMMPS *lmp, int narg, char **arg) :

  Fix(lmp, narg, arg),

  rstyle(NULL), ids(NULL), kstart(NULL), kstop(NULL), target(NULL),

  rstyle(NULL), mult(NULL), ids(NULL), kstart(NULL), kstop(NULL), target(NULL),

  cos_target(NULL), sin_target(NULL)

{

  if (narg < 4) error->all(FLERR,"Illegal fix restrain command");
@@ -65,6 +65,7 @@ FixRestrain::FixRestrain(LAMMPS *lmp, int narg, char **arg) : 
    if (nrestrain == maxrestrain) {

      maxrestrain += DELTA;

      memory->grow(rstyle,maxrestrain,"restrain:rstyle");

      memory->grow(mult,maxrestrain,"restrain:mult");

      memory->grow(ids,maxrestrain,4,"restrain:ids");

      memory->grow(kstart,maxrestrain,"restrain:kstart");

      memory->grow(kstop,maxrestrain,"restrain:kstop");
@@ -96,6 +97,7 @@ FixRestrain::FixRestrain(LAMMPS *lmp, int narg, char **arg) : 
    } else if (strcmp(arg[iarg],"dihedral") == 0) {

      if (iarg+8 > narg) error->all(FLERR,"Illegal fix restrain command");

      rstyle[nrestrain] = DIHEDRAL;

      mult[nrestrain]   = 1;

      ids[nrestrain][0] = force->inumeric(FLERR,arg[iarg+1]);

      ids[nrestrain][1] = force->inumeric(FLERR,arg[iarg+2]);

      ids[nrestrain][2] = force->inumeric(FLERR,arg[iarg+3]);
@@ -107,6 +109,13 @@ FixRestrain::FixRestrain(LAMMPS *lmp, int narg, char **arg) : 
      cos_target[nrestrain] = cos(target[nrestrain]);

      sin_target[nrestrain] = sin(target[nrestrain]);

      iarg += 8;

      if ((iarg < narg) && (strcmp("mult",arg[iarg]) == 0)) {

        if (iarg+1 > narg) error->all(FLERR,"Illegal fix restrain command");

        mult[nrestrain] = force->inumeric(FLERR,arg[iarg+1]);

        if (mult[nrestrain] < 0)

          error->all(FLERR,"Illegal fix restrain command");

        iarg += 2;

      }

    } else error->all(FLERR,"Illegal fix restrain command");



    nrestrain++;
@@ -123,6 +132,7 @@ FixRestrain::FixRestrain(LAMMPS *lmp, int narg, char **arg) : 
FixRestrain::~FixRestrain()

{

  memory->destroy(rstyle);

  memory->destroy(mult);

  memory->destroy(ids);

  memory->destroy(kstart);

  memory->destroy(kstop);
@@ -410,7 +420,7 @@ void FixRestrain::restrain_angle(int m) 


void FixRestrain::restrain_dihedral(int m)

{

  int i1,i2,i3,i4,i,mult;

  int i1,i2,i3,i4,i;

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

  double f1[3],f2[3],f3[3],f4[3];

  double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,rginv,ra2inv,rb2inv,rabinv;
@@ -534,11 +544,10 @@ void FixRestrain::restrain_dihedral(int m) 
  if (c > 1.0) c = 1.0;

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



  mult = 1;  // multiplicity

  p = 1.0;

  df1 = 0.0;



  for (i = 0; i < mult; i++) {

  for (i = 0; i < mult[m]; i++) {

    ddf1 = p*c - df1*s;

    df1 = p*s + df1*c;

    p = ddf1;
@@ -546,7 +555,7 @@ void FixRestrain::restrain_dihedral(int m) 


  p = p*cos_target[m] + df1*sin_target[m];

  df1 = df1*cos_target[m] - ddf1*sin_target[m];

  df1 *= -mult;

  df1 *= -mult[m];

  p += 1.0;



  energy += k * p;

src/fix_restrain.h

+1 −0
Original line number Diff line number Diff line
@@ -41,6 +41,7 @@ class FixRestrain : public Fix { 
  int ilevel_respa;

  int nrestrain,maxrestrain;

  int *rstyle;

  int *mult;

  int **ids;

  double *kstart,*kstop,*target;

  double *cos_target,*sin_target;

CRA Git | Maintained and supported by SUSTech CRA and CCSE