Commit ebce76c7 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

updated and slightly refactored tabulation for vashishta pair style 

- tables are now dimensioned by nelements instead of ntypes
- tables are only created if used
- correctly identify max size of table
- add test for illegal cutoff for tabulation
- allocated memory for tables is accounted for
- add example input using 16-bit tables
parent bf59c976

examples/vashishta/in.indiumphosphide-tabulated

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+76 −0
Original line number Diff line number Diff line 
# calculate the energy volume curve for InP zincblende



# define volume range and filename



variable	ndelta equal 100

variable	volatom_min equal 20.0

variable	volatom_max equal 29.0

variable	evsvolfile string evsvol.dat



# set up cell 



units		metal

 

boundary	p p p



# setup loop variables for box volume



variable	amin equal ${volatom_min}^(1/3)*2

variable 	delta equal (${volatom_max}-${volatom_min})/${ndelta} 

variable	scale equal (${delta}/v_volatom+1)^(1/3)



# set up 8 atom InP zincblende unit cell



lattice diamond ${amin}



region		box prism &

	 	0 1 &

		0 1 &

		0 1 &

		0 0 0



create_box	2 box



create_atoms	1	box       &

			basis 5 2 &

			basis 6 2 &

			basis 7 2 &

			basis 8 2



mass 		1 114.76

mass 		2 30.98



# choose potential



pair_style	vashishta

pair_coeff 	* * InP.vashishta In P

pair_modify     table 16



# setup neighbor style



neighbor 	1.0 nsq

neigh_modify 	once no every 1 delay 0 check yes



# setup output



thermo_style 	custom step temp pe press vol

thermo_modify 	norm no

variable 	volatom equal vol/atoms

variable 	eatom equal pe/atoms

print 		"# Volume [A^3/atom] Energy [eV/atom]" file ${evsvolfile}



# loop over range of volumes



label 		loop

variable 	i loop ${ndelta}



change_box 	all x scale ${scale} y scale ${scale} z scale ${scale} remap



# calculate energy

# no energy minimization needed for zincblende

 

run 		0

print 		"${volatom} ${eatom}" append ${evsvolfile}



next 		i

jump 		SELF loop

examples/vashishta/in.sio2-tabulated

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+29 −0
Original line number Diff line number Diff line 
# test Vashishta potential for quartz



units		metal

boundary	p p p



atom_style	atomic



read_data	data.quartz



replicate       4 4 4

velocity	all create 2000.0 277387 mom yes

displace_atoms	all move 0.05 0.9 0.4 units box



pair_style 	vashishta

pair_coeff	* *  SiO.1990.vashishta Si O

pair_modify	table 16



neighbor	0.3 bin

neigh_modify	delay 10



fix		1 all nve

thermo		10

timestep	0.001



#dump		1 all cfg 10 *.cfg mass type xs ys zs vx vy vz fx fy fz

#dump_modify	1 element Si O



run		100

src/MANYBODY/pair_vashishta.cpp

+45 −39
Original line number Diff line number Diff line
@@ -97,9 +97,8 @@ void PairVashishta::modify_params(int narg, char **arg) 
      if (iarg+2 > narg) error->all(FLERR,"Illegal pair_modify command");



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

      if (nTablebits > sizeof(float)*CHAR_BIT) {

        error->all(FLERR,"Too many total bits for bitmapped lookup table");

      }

      if ((nTablebits < 0) || (nTablebits > sizeof(int)*CHAR_BIT-1))

        error->all(FLERR,"Illegal interpolation table size");



      if (nTablebits == 0) {

        useTable = false;
@@ -112,11 +111,12 @@ void PairVashishta::modify_params(int narg, char **arg) 
      if (iarg+2 > narg) error->all(FLERR,"Illegal pair_modify command");

      

      tabinner = force->numeric(FLERR,arg[iarg+1]);

      if (tabinner <= 0.0)

        error->all(FLERR,"Illegal inner cutoff for tabulation");

      iarg += 2;

    }

  }



  createTable();

  updateTables();

}



void PairVashishta::validateNeigh3Body() {
@@ -129,40 +129,34 @@ void PairVashishta::validateNeigh3Body() { 
    }

}



void PairVashishta::createTable()

void PairVashishta::updateTables()

{

  int ntypes = atom->ntypes+1;

  tabinnersq = tabinner*tabinner;

  memory->destroy(forceTable);

  memory->destroy(potentialTable);

  forceTable = NULL;

  potentialTable = NULL;



  int ntable = 1;

  for (int i = 0; i < nTablebits; i++) ntable *= 2;

  if (!useTable) return;



  int ntable = 1<<nTablebits;

  tabinnersq = tabinner*tabinner;



  deltaR2 = (cutmax*cutmax - tabinnersq) / (ntable-1);

  oneOverDeltaR2 = 1.0/deltaR2;



  memory->destroy(forceTable);

  memory->destroy(potentialTable);

  memory->create(forceTable,ntypes,ntypes,ntable+1,"pair:vashishta:forceTable");

  memory->create(potentialTable,ntypes,ntypes,ntable+1,"pair:vashishta:potentialTable");



  for (int ii = 0; ii < ntypes; ii++) {

    int i = map[ii];

    for (int jj = 0; jj < ntypes; jj++) {

      int j = map[jj];

      if (i < 0 || j < 0 || ii == 0 || jj == 0) {

        for(int tableIndex=0; tableIndex<=ntable; tableIndex++) {

            forceTable[ii][jj][tableIndex] = 0;

            potentialTable[ii][jj][tableIndex] = 0;

        }

      } else {

  memory->create(forceTable,nelements,nelements,ntable+1,"pair:vashishta:forceTable");

  memory->create(potentialTable,nelements,nelements,ntable+1,"pair:vashishta:potentialTable");



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

    for (int j = 0; j < nelements; j++) {

      int ijparam = elem2param[i][j][j];

        for(int tableIndex=0; tableIndex<=ntable; tableIndex++) {

            double rsq = tabinnersq + tableIndex*deltaR2;

      for(int idx=0; idx <= ntable; idx++) {

        double rsq = tabinnersq + idx*deltaR2;

        double fpair, eng;

            twobody(&params[ijparam], rsq, fpair, 1, eng, false /* Don't ask for tabulated since we are generating it now*/ );

            forceTable[ii][jj][tableIndex] = fpair;

            potentialTable[ii][jj][tableIndex] = eng;

        }

        // call analytical version of two-body term function

        twobody(&params[ijparam], rsq, fpair, 1, eng, false);

        forceTable[i][j][idx] = fpair;

        potentialTable[i][j][idx] = eng;

      }

    }

  }
@@ -642,7 +636,7 @@ void PairVashishta::setup_params() 
    if (params[m].r0 > cutmax) cutmax = params[m].r0;

  }



  createTable();

  updateTables();

}



/* ---------------------------------------------------------------------- */
@@ -660,12 +654,12 @@ void PairVashishta::twobody(Param *param, double rsq, double &fforce, 
    int tableIndex = (rsq - tabinnersq)*oneOverDeltaR2;

    double fraction = (rsq - tabinnersq)*oneOverDeltaR2 - tableIndex; // double - int will only keep the 0.xxxx part



    double force0 = forceTable[param->ielement+1][param->jelement+1][tableIndex];

    double force1 = forceTable[param->ielement+1][param->jelement+1][tableIndex+1];

    double force0 = forceTable[param->ielement][param->jelement][tableIndex];

    double force1 = forceTable[param->ielement][param->jelement][tableIndex+1];

    fforce = (1.0 - fraction)*force0 + fraction*force1; // force is linearly interpolated between the two values

    if(evflag) {

        double energy0 = potentialTable[param->ielement+1][param->jelement+1][tableIndex];

        double energy1 = potentialTable[param->ielement+1][param->jelement+1][tableIndex+1];

        double energy0 = potentialTable[param->ielement][param->jelement][tableIndex];

        double energy1 = potentialTable[param->ielement][param->jelement][tableIndex+1];

        eng = (1.0 - fraction)*energy0 + fraction*energy1;

    }

  } else {
@@ -747,3 +741,15 @@ void PairVashishta::threebody(Param *paramij, Param *paramik, Param *paramijk, 


  if (eflag) eng = facrad;

}



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

 *  add memory usage for tabulation

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



double PairVashishta::memory_usage()

{

  double bytes = Pair::memory_usage();

  if (useTable)

    bytes += 2*nelements*nelements*sizeof(double)*(1<<nTablebits);

  return bytes;

}

src/MANYBODY/pair_vashishta.h

+2 −1
Original line number Diff line number Diff line
@@ -34,6 +34,7 @@ class PairVashishta : public Pair { 
  void coeff(int, char **);

  virtual double init_one(int, int);

  virtual void init_style();

  virtual double memory_usage();



 protected:

  struct Param {
@@ -71,7 +72,7 @@ class PairVashishta : public Pair { 
  virtual void allocate();

  void read_file(char *);

  void setup_params();

  void createTable();

  void updateTables();

  void validateNeigh3Body();

  void twobody(Param *, double, double &, int, double &, bool tabulated = false);

  void threebody(Param *, Param *, Param *, double, double, double *, double *,

src/USER-OMP/pair_vashishta_omp.cpp

+1 −1

File changed.

Contains only whitespace changes.

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