Commit e9a2d5ab authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1752 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent 8a08b7f3

src/COLLOID/pair_lubricate.cpp

+70 −23
Original line number Diff line number Diff line
@@ -28,8 +28,8 @@ 
#include "neigh_request.h"

#include "update.h"

#include "memory.h"

#include "random_mars.h"

#include "error.h"

#include "domain.h"



using namespace LAMMPS_NS;
@@ -41,6 +41,8 @@ using namespace LAMMPS_NS; 
PairLubricate::PairLubricate(LAMMPS *lmp) : Pair(lmp)

{

  single_enable = 0;



  random = NULL;

}



/* ---------------------------------------------------------------------- */
@@ -54,6 +56,7 @@ PairLubricate::~PairLubricate() 
    memory->destroy_2d_double_array(cut);

    memory->destroy_2d_double_array(cut_inner);

  }

  delete random;

}



/* ---------------------------------------------------------------------- */
@@ -61,8 +64,8 @@ PairLubricate::~PairLubricate() 
void PairLubricate::compute(int eflag, int vflag)

{

  int i,j,ii,jj,inum,jnum,itype,jtype;

  double xtmp,ytmp,ztmp,delx,dely,delz,fpair,fx,fy,fz;

  double rsq,r,h_sep,radi;

  double xtmp,ytmp,ztmp,delx,dely,delz,fpair,fx,fy,fz,tx,ty,tz;

  double rsq,r,h_sep,radi,tfmag;

  double vr1,vr2,vr3,vnnr,vn1,vn2,vn3;

  double vt1,vt2,vt3,w1,w2,w3,v_shear1,v_shear2,v_shear3;

  double omega_t_1,omega_t_2,omega_t_3;
@@ -88,6 +91,9 @@ void PairLubricate::compute(int eflag, int vflag) 
  int omega_flag = atom->omega_flag;

  double vxmu2f = force->vxmu2f;



  double prethermostat = sqrt(2.0 * force->boltz * t_target / update->dt);

  prethermostat *= sqrt(force->vxmu2f/force->ftm2v/force->mvv2e);



  inum = list->inum;

  ilist = list->ilist;

  numneigh = list->numneigh;
@@ -167,7 +173,7 @@ void PairLubricate::compute(int eflag, int vflag) 
	omega_t_2 = w2 - dely*(dely*w2) / rsq;

	omega_t_3 = w3 - delz*(delz*w3) / rsq;



        // n x omega_t

        // n X omega_t



        n_cross_omega_t_1 =  (dely*omega_t_3 - delz*omega_t_2) / r;

        n_cross_omega_t_2 =  -(delx*omega_t_3 - delz*omega_t_1) / r;
@@ -199,17 +205,16 @@ void PairLubricate::compute(int eflag, int vflag) 
        h_sep = r - 2.0*radi;



	if (flag1)

	  a_squeeze = vxmu2f * 

	    (3.0*PI*mu*2.0*radi/2.0) * (2.0*radi/4.0/h_sep); 

	  a_squeeze = (3.0*PI*mu*2.0*radi/2.0) * (2.0*radi/4.0/h_sep);

	if (flag2) 

	  a_shear = vxmu2f * (PI*mu*2.*radi/2.0) *

	  a_shear = (PI*mu*2.*radi/2.0) *

	    log(2.0*radi/2.0/h_sep)*(2.0*radi+h_sep)*(2.0*radi+h_sep)/4.0;

	if (flag3) 

	  a_pump = vxmu2f * (PI*mu*pow(2.0*radi,4)/8.0) *

	  a_pump = (PI*mu*pow(2.0*radi,4)/8.0) *

	    ((3.0/20.0) * log(2.0*radi/2.0/h_sep) + 

	     (63.0/250.0) * (h_sep/2.0/radi) * log(2.0*radi/2.0/h_sep));

	if (flag4)

	  a_twist = vxmu2f * (PI*mu*pow(2.0*radi,4)/4.0) *

	  a_twist = (PI*mu*pow(2.0*radi,4)/4.0) *

	    (h_sep/2.0/radi) * log(2.0/(2.0*h_sep));



        if (h_sep >= cut_inner[itype][jtype]) {
@@ -219,16 +224,37 @@ void PairLubricate::compute(int eflag, int vflag) 
	    (2.0/r)*a_shear*n_cross_omega_t_2;

          fz = -a_squeeze*vn3 - a_shear*(2.0/r)*(2.0/r)*vt3 +

	    (2.0/r)*a_shear*n_cross_omega_t_3;

	  fx *= vxmu2f;

	  fy *= vxmu2f;

	  fz *= vxmu2f;



	  // add in thermostat force



	  torque[i][0] += -(2.0/r)*a_shear*v_shear1 - a_shear*omega_t_1 - 

	  tfmag = prethermostat*sqrt(a_squeeze)*(random->uniform()-0.5);

	  fx -= tfmag * delx/r;

	  fy -= tfmag * dely/r;

	  fz -= tfmag * delz/r;

	  

	  tx = -(2.0/r)*a_shear*v_shear1 - a_shear*omega_t_1 - 

	    a_pump*P_dot_wrel_1 - a_twist*wn1;

	  torque[i][1] += -(2.0/r)*a_shear*v_shear2 - a_shear*omega_t_2 - 

	  ty = -(2.0/r)*a_shear*v_shear2 - a_shear*omega_t_2 - 

	    a_pump*P_dot_wrel_2 - a_twist*wn2;

	  torque[i][2] += -(2.0/r)*a_shear*v_shear3 - a_shear*omega_t_3 - 

	  tz = -(2.0/r)*a_shear*v_shear3 - a_shear*omega_t_3 - 

	    a_pump*P_dot_wrel_3 - a_twist*wn3;

	  torque[i][0] += vxmu2f * tx;

	  torque[i][1] += vxmu2f * ty;

	  torque[i][2] += vxmu2f * tz;



        } else {

	  fpair = -vnnr*(3.0*PI*mu*radi/2.0)*radi/4.0/cut_inner[itype][jtype];

	  a_squeeze = (3.0*PI*mu*2.0*radi/2.0) * 

	    (2.0*radi/4.0/cut_inner[itype][jtype]);

	  fpair = -a_squeeze*vnnr;

	  fpair *= vxmu2f;



	  // add in thermostat force



	  fpair -= prethermostat*sqrt(a_squeeze)*(random->uniform()-0.5);



	  fx = fpair * delx/r;

	  fy = fpair * dely/r;

	  fz = fpair * delz/r;
@@ -244,12 +270,15 @@ void PairLubricate::compute(int eflag, int vflag) 
	  f[j][2] -= fz;



	  if (h_sep >= cut_inner[itype][jtype]) {

	    torque[j][0] += -(2.0/r)*a_shear*v_shear1 - a_shear*omega_t_1 + 

	    tx = -(2.0/r)*a_shear*v_shear1 - a_shear*omega_t_1 + 

	      a_pump*P_dot_wrel_1 + a_twist*wn1;

	    torque[j][1] += -(2.0/r)*a_shear*v_shear2 - a_shear*omega_t_2 + 

	    ty = -(2.0/r)*a_shear*v_shear2 - a_shear*omega_t_2 + 

	      a_pump*P_dot_wrel_2 + a_twist*wn2;

	    torque[j][2] += -(2.0/r)*a_shear*v_shear3 - a_shear*omega_t_3 + 

	    tz = -(2.0/r)*a_shear*v_shear3 - a_shear*omega_t_3 + 

	      a_pump*P_dot_wrel_3 + a_twist*wn3;

	    torque[j][0] += vxmu2f * tx;

	    torque[j][1] += vxmu2f * ty;

	    torque[j][2] += vxmu2f * tz;

	  }

	}
@@ -288,7 +317,7 @@ void PairLubricate::allocate() 


void PairLubricate::settings(int narg, char **arg)

{

  if (narg != 7) error->all("Illegal pair_style command");

  if (narg != 9) error->all("Illegal pair_style command");



  mu = atof(arg[0]);

  flag1 = atoi(arg[1]);
@@ -297,6 +326,8 @@ void PairLubricate::settings(int narg, char **arg) 
  flag4 = atoi(arg[4]);

  cut_inner_global = atof(arg[5]);

  cut_global = atof(arg[6]);

  t_target = atof(arg[7]);

  seed = atoi(arg[8]);



  // reset cutoffs that have been explicitly set
@@ -309,6 +340,11 @@ void PairLubricate::settings(int narg, char **arg) 
	  cut[i][j] = cut_global;

	}

  }



  // initialize Marsaglia RNG with processor-unique seed



  delete random;

  random = new RanMars(lmp,seed + comm->me);

}



/* ----------------------------------------------------------------------
@@ -446,6 +482,8 @@ void PairLubricate::write_restart_settings(FILE *fp) 
  fwrite(&flag4,sizeof(int),1,fp);

  fwrite(&cut_inner_global,sizeof(double),1,fp);

  fwrite(&cut_global,sizeof(double),1,fp);

  fwrite(&t_target,sizeof(double),1,fp);

  fwrite(&seed,sizeof(int),1,fp);

  fwrite(&offset_flag,sizeof(int),1,fp);

  fwrite(&mix_flag,sizeof(int),1,fp);

}
@@ -465,6 +503,8 @@ void PairLubricate::read_restart_settings(FILE *fp) 
    fread(&flag4,sizeof(int),1,fp);

    fread(&cut_inner_global,sizeof(double),1,fp);

    fread(&cut_global,sizeof(double),1,fp);

    fread(&t_target, sizeof(double),1,fp);

    fread(&seed, sizeof(int),1,fp);

    fread(&offset_flag,sizeof(int),1,fp);

    fread(&mix_flag,sizeof(int),1,fp);

  }
@@ -475,6 +515,13 @@ void PairLubricate::read_restart_settings(FILE *fp) 
  MPI_Bcast(&flag4,1,MPI_INT,0,world);

  MPI_Bcast(&cut_inner_global,1,MPI_DOUBLE,0,world);

  MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);

  MPI_Bcast(&t_target,1,MPI_DOUBLE,0,world);

  MPI_Bcast(&seed,1,MPI_INT,0,world);

  MPI_Bcast(&offset_flag,1,MPI_INT,0,world);

  MPI_Bcast(&mix_flag,1,MPI_INT,0,world);



  // additional setup based on restart parameters



  delete random;

  random = new RanMars(lmp,seed + comm->me);

}

src/COLLOID/pair_lubricate.h

+5 −3
Original line number Diff line number Diff line
@@ -34,9 +34,12 @@ class PairLubricate : public Pair { 


 protected:

  double cut_inner_global,cut_global;

  double **cut_inner,**cut;

  double mu;

  double t_target,mu;

  int flag1,flag2,flag3,flag4;

  int seed;

  double **cut_inner,**cut;



  class RanMars *random;



  void allocate();

};
@@ -44,4 +47,3 @@ class PairLubricate : public Pair { 
}



#endif

src/fix_npt.cpp

+0 −1
Original line number Diff line number Diff line
@@ -63,7 +63,6 @@ FixNPT::FixNPT(LAMMPS *lmp, int narg, char **arg) : 
  double p_period[3];

  if (strcmp(arg[6],"xyz") == 0) {

    if (narg < 10) error->all("Illegal fix npt command");



    press_couple = XYZ;

    p_start[0] = p_start[1] = p_start[2] = atof(arg[7]);

    p_stop[0] = p_stop[1] = p_stop[2] = atof(arg[8]);

CRA Git | Maintained and supported by SUSTech CRA and CCSE