Commit 393337e7 authored by sjplimp's avatar sjplimp Committed by GitHub
Browse files

Merge pull request #226 from akohlmey/pair-gauss-mixing 

add mixing support for pair styles gauss and gauss/cut
parents e0ed218c 7b7cb297

doc/src/pair_gauss.txt

+25 −2
Original line number Diff line number Diff line
@@ -106,8 +106,31 @@ more instructions on how to use the accelerated styles effectively. 


[Mixing, shift, table, tail correction, restart, rRESPA info]:



These pair styles do not support mixing. Thus, coefficients for all

I,J pairs must be specified explicitly.

For atom type pairs I,J and I != J, the A, B, H, sigma_h, r_mh

parameters, and the cutoff distance for these pair styles can be mixed:

A (energy units)

sqrt(1/B) (distance units, see below)

H (energy units)

sigma_h (distance units)

r_mh (distance units)

cutoff (distance units):ul



The default mix value is {geometric}.

Only {arithmetic} and {geometric} mix values are supported.

See the "pair_modify" command for details.



The A and H parameters are mixed using the same rules normally

used to mix the "epsilon" parameter in a Lennard Jones interaction.

The sigma_h, r_mh, and the cutoff distance are mixed using the same

rules used to mix the "sigma" parameter in a Lennard Jones interaction.

The B parameter is converted to a distance (sigma), before mixing

(using sigma=B^-0.5), and converted back to a coefficient

afterwards (using B=sigma^2).

Negative A values are converted to positive A values (using abs(A))

before mixing, and converted back after mixing

(by multiplying by sign(Ai)*sign(Aj)).

This way, if either particle is repulsive (if Ai<0 or Aj<0),

then the default interaction between both particles will be repulsive.



The {gauss} style does not support the "pair_modify"_pair_modify.html

shift option. There is no effect due to the Gaussian well beyond the

src/USER-MISC/pair_gauss_cut.cpp

+37 −2
Original line number Diff line number Diff line
@@ -39,6 +39,7 @@ using namespace MathConst; 
PairGaussCut::PairGaussCut(LAMMPS *lmp) : Pair(lmp)

{

  respa_enable = 0;

  writedata = 1;

}



/* ---------------------------------------------------------------------- */
@@ -96,7 +97,6 @@ void PairGaussCut::compute(int eflag, int vflag) 


    for (jj = 0; jj < jnum; jj++) {

      j = jlist[jj];



      factor_lj = special_lj[sbmask(j)];

      j &= NEIGHMASK;
@@ -221,7 +221,21 @@ void PairGaussCut::coeff(int narg, char **arg) 


double PairGaussCut::init_one(int i, int j)

{

  if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");

  if (setflag[i][j] == 0) {

    hgauss[i][j] = mix_energy(fabs(hgauss[i][i]), fabs(hgauss[j][j]),

			      fabs(sigmah[i][i]), fabs(sigmah[j][j]));



    // If either of the particles is repulsive (ie, if hgauss > 0),

    // then the interaction between both is repulsive.

    double sign_hi = (hgauss[i][i] >= 0.0) ? 1.0 : -1.0;

    double sign_hj = (hgauss[j][j] >= 0.0) ? 1.0 : -1.0;

    hgauss[i][j] *= MAX(sign_hi, sign_hj);



    sigmah[i][j] = mix_distance(sigmah[i][i], sigmah[j][j]);

    rmh[i][j] = mix_distance(rmh[i][i], rmh[j][j]);

    cut[i][j] = mix_distance(cut[i][i], cut[j][j]);

  }



  pgauss[i][j] = hgauss[i][j] / sqrt(MY_2PI) / sigmah[i][j];



  if (offset_flag) {
@@ -334,6 +348,27 @@ void PairGaussCut::read_restart_settings(FILE *fp) 
  MPI_Bcast(&mix_flag,1,MPI_INT,0,world);

}



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

   proc 0 writes to data file

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



void PairGaussCut::write_data(FILE *fp)

{

  for (int i = 1; i <= atom->ntypes; i++)

    fprintf(fp,"%d %g %g %g\n",i,hgauss[i][i],rmh[i][i],sigmah[i][i]);

}



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

   proc 0 writes all pairs to data file

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



void PairGaussCut::write_data_all(FILE *fp)

{

  for (int i = 1; i <= atom->ntypes; i++)

    for (int j = i; j <= atom->ntypes; j++)

      fprintf(fp,"%d %d %g %g %g %g\n",i,j,hgauss[i][j],rmh[i][j],sigmah[i][j],cut[i][j]);

}



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



double PairGaussCut::single(int i, int j, int itype, int jtype, double rsq,

src/USER-MISC/pair_gauss_cut.h

+2 −0
Original line number Diff line number Diff line
@@ -42,6 +42,8 @@ class PairGaussCut : public Pair { 
  virtual void read_restart(FILE *);

  virtual void write_restart_settings(FILE *);

  virtual void read_restart_settings(FILE *);

  virtual void write_data(FILE *fp);

  virtual void write_data_all(FILE *fp);



  virtual double memory_usage();

src/pair_gauss.cpp

+45 −9
Original line number Diff line number Diff line
@@ -38,6 +38,7 @@ PairGauss::PairGauss(LAMMPS *lmp) :Pair(lmp) 
{

  nextra = 1;

  pvector = new double[1];

  writedata = 1;

}



/* ---------------------------------------------------------------------- */
@@ -217,12 +218,27 @@ void PairGauss::coeff(int narg, char **arg) 


double PairGauss::init_one(int i, int j)

{

  if (setflag[i][j] == 0) {

    double sign_bi = (b[i][i] >= 0.0) ? 1.0 : -1.0;

    double sign_bj = (b[j][j] >= 0.0) ? 1.0 : -1.0;

    double si = sqrt(0.5/fabs(b[i][i]));

    double sj = sqrt(0.5/fabs(b[j][j]));

    double sij = mix_distance(si, sj);

    b[i][j] = 0.5 / (sij*sij);

    b[i][j] *= MAX(sign_bi, sign_bj);



    // Negative "a" values are useful for simulating repulsive particles.

    // If either of the particles is repulsive (a<0), then the

    // interaction between both is repulsive.

    double sign_ai = (a[i][i] >= 0.0) ? 1.0 : -1.0;

    double sign_aj = (a[j][j] >= 0.0) ? 1.0 : -1.0;

    a[i][j] = mix_energy(fabs(a[i][i]), fabs(a[j][j]), si, sj);

    a[i][j] *= MIN(sign_ai, sign_aj);



    cut[i][j] = mix_distance(cut[i][i],cut[j][j]);

  }



  // This error is triggered when ti is performed on lj/cut tail

  // in presence of extra atom type for tether sites

  // "i = 2 j = 1 ERROR: All pair coeffs are not set (pair_gauss.cpp:223)"

  //  if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");



  // cutoff correction to energy

  if (offset_flag) offset[i][j] = a[i][j]*exp(-b[i][j]*cut[i][j]*cut[i][j]);

  else offset[i][j] = 0.0;
@@ -260,7 +276,6 @@ void PairGauss::write_restart(FILE *fp) 
void PairGauss::read_restart(FILE *fp)

{

  read_restart_settings(fp);



  allocate();



  int i,j;
@@ -309,6 +324,27 @@ void PairGauss::read_restart_settings(FILE *fp) 
  MPI_Bcast(&mix_flag,1,MPI_INT,0,world);

}



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

   proc 0 writes to data file

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



void PairGauss::write_data(FILE *fp)

{

  for (int i = 1; i <= atom->ntypes; i++)

    fprintf(fp,"%d %g %g\n",i,a[i][i],b[i][i]);

}



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

   proc 0 writes all pairs to data file

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



void PairGauss::write_data_all(FILE *fp)

{

  for (int i = 1; i <= atom->ntypes; i++)

    for (int j = i; j <= atom->ntypes; j++)

      fprintf(fp,"%d %d %g %g %g\n",i,j,a[i][j],b[i][j],cut[i][j]);

}



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



double PairGauss::single(int i, int j, int itype, int jtype, double rsq,

src/pair_gauss.h

+2 −0
Original line number Diff line number Diff line
@@ -36,6 +36,8 @@ class PairGauss : public Pair { 
  void read_restart(FILE *);

  void write_restart_settings(FILE *);

  void read_restart_settings(FILE *);

  void write_data(FILE *fp);

  void write_data_all(FILE *fp);

  double single(int, int, int, int, double, double, double, double &);

  void *extract(const char *, int &);

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