Commit 6ba8c459 authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1582 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent c012684a

src/compute_pressure.cpp

+1 −0
Original line number Diff line number Diff line
@@ -109,6 +109,7 @@ void ComputePressure::init() 
  dimension = domain->dimension;



  // set temperature used by pressure

  // must be done in init() since user can change it via modify command



  int icompute = modify->find_compute(id_pre);

  if (icompute < 0) error->all("Could not find compute pressure temp ID");

src/fix_langevin.cpp

+2 −8
Original line number Diff line number Diff line
@@ -58,7 +58,6 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) : 
  flagx = flagy = flagz = 1;

  for (int i = 1; i <= atom->ntypes; i++) ratio[i] = 1.0;

  iregion = -1;

  scalefactor = 1.0;



  int iarg = 7;

  while (iarg < narg) {
@@ -81,11 +80,6 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) : 
      iregion = domain->find_region(arg[iarg+1]);

      if (iregion == -1) error->all("Fix langevin region ID does not exist");

      iarg += 2;

    } else if (strcmp(arg[iarg],"weight") == 0) {

      if (iarg+2 > narg) error->all("Illegal fix langevin command");

      scalefactor = atof(arg[iarg+1]);

      if (scalefactor <= 0.0) error->all("Illegal fix langevin command");

      iarg += 2;

    } else error->all("Illegal fix langevin command");

  }

}
@@ -121,7 +115,7 @@ void FixLangevin::init() 


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

    gfactor1[i] = - atom->mass[i] / t_period / force->ftm2v;

    gfactor2[i] = scalefactor * sqrt(atom->mass[i]) * 

    gfactor2[i] = sqrt(atom->mass[i]) * 

      sqrt(24.0*force->boltz/t_period/update->dt/force->mvv2e) / force->ftm2v;

    gfactor1[i] *= 1.0/ratio[i];

    gfactor2[i] *= 1.0/sqrt(ratio[i]);
@@ -210,7 +204,7 @@ void FixLangevin::reset_target(double t_new) 
void FixLangevin::reset_dt()

{

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

    gfactor2[i] = scalefactor * sqrt(atom->mass[i]) * 

    gfactor2[i] = sqrt(atom->mass[i]) * 

      sqrt(24.0*force->boltz/t_period/update->dt/force->mvv2e) / force->ftm2v;

    gfactor2[i] *= 1.0/sqrt(ratio[i]);

  }

src/fix_langevin.h

+0 −1
Original line number Diff line number Diff line
@@ -34,7 +34,6 @@ class FixLangevin : public Fix { 
  double t_start,t_stop,t_period;

  int flagx,flagy,flagz,iregion;

  double *gfactor1,*gfactor2,*ratio;

  double scalefactor;



  int nlevels_respa;

  class RanMars *random;

src/thermo.cpp

+34 −19
Original line number Diff line number Diff line
@@ -121,7 +121,8 @@ Thermo::Thermo(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) 
  rotate_dipole = NULL;

  rotate_gran = NULL;



  index_temp = index_press = index_pe = index_drot = index_grot = -1;

  index_temp = index_press_scalar = index_press_vector = index_pe = -1;

  index_drot = index_grot = -1;

  internal_drot = internal_grot = 0;



  id_temp = (char *) "thermo_temp";
@@ -263,7 +264,8 @@ void Thermo::init() 
  // set ptrs to keyword-specific Compute objects



  if (index_temp >= 0) temperature = computes[index_temp];

  if (index_press >= 0) pressure = computes[index_press];

  if (index_press_scalar >= 0) pressure = computes[index_press_scalar];

  if (index_press_vector >= 0) pressure = computes[index_press_vector];

  if (index_pe >= 0) pe = computes[index_pe];

  if (index_drot >= 0) rotate_dipole = computes[index_drot];

  if (index_grot >= 0) rotate_gran = computes[index_grot];
@@ -400,7 +402,7 @@ void Thermo::modify_params(int narg, char **arg) 
      id_compute[index_temp] = new char[n];

      strcpy(id_compute[index_temp],arg[iarg+1]);



      int icompute = modify->find_compute(id_compute[index_temp]);

      int icompute = modify->find_compute(arg[iarg+1]);

      if (icompute < 0) error->all("Could not find thermo_modify temp ID");

      temperature = modify->compute[icompute];
@@ -412,8 +414,11 @@ void Thermo::modify_params(int narg, char **arg) 
      // reset id_pre of pressure to new temp ID

      // either pressure currently being used by thermo or "thermo_press"



      if (index_press >= 0) {

	icompute = modify->find_compute(id_compute[index_press]);

      if (index_press_scalar >= 0) {

	icompute = modify->find_compute(id_compute[index_press_scalar]);

	if (icompute < 0) error->all("Press ID for thermo does not exist");

      } else if (index_press_vector >= 0) {

	icompute = modify->find_compute(id_compute[index_press_vector]);

	if (icompute < 0) error->all("Press ID for thermo does not exist");

      } else icompute = modify->find_compute((char *) "thermo_press");
@@ -425,13 +430,23 @@ void Thermo::modify_params(int narg, char **arg) 


    } else if (strcmp(arg[iarg],"press") == 0) {

      if (iarg+2 > narg) error->all("Illegal thermo_modify command");

      if (index_press < 0) error->all("Thermo style does not use press");

      delete [] id_compute[index_press];

      if (index_press_scalar < 0 && index_press_vector < 0)

	error->all("Thermo style does not use press");



      if (index_press_scalar >= 0) {

	delete [] id_compute[index_press_scalar];

	int n = strlen(arg[iarg+1]) + 1;

      id_compute[index_press] = new char[n];

      strcpy(id_compute[index_press],arg[iarg+1]);

	id_compute[index_press_scalar] = new char[n];

	strcpy(id_compute[index_press_scalar],arg[iarg+1]);

      }

      if (index_press_vector >= 0) {

	delete [] id_compute[index_press_vector];

	int n = strlen(arg[iarg+1]) + 1;

	id_compute[index_press_vector] = new char[n];

	strcpy(id_compute[index_press_vector],arg[iarg+1]);

      }



      int icompute = modify->find_compute(id_compute[index_press]);

      int icompute = modify->find_compute(arg[iarg+1]);

      if (icompute < 0) error->all("Could not find thermo_modify press ID");

      pressure = modify->compute[icompute];
@@ -629,7 +644,7 @@ void Thermo::parse_fields(char *str) 
      index_temp = add_compute(id_temp,0);

    } else if (strcmp(word,"press") == 0) {

      addfield("Press",&Thermo::compute_press,FLOAT);

      index_press = add_compute(id_press,0);

      index_press_scalar = add_compute(id_press,0);

    } else if (strcmp(word,"pe") == 0) {

      addfield("PotEng",&Thermo::compute_pe,FLOAT);

      index_pe = add_compute(id_pe,0);
@@ -643,7 +658,7 @@ void Thermo::parse_fields(char *str) 
    } else if (strcmp(word,"enthalpy") == 0) {

      addfield("Enthalpy",&Thermo::compute_enthalpy,FLOAT);

      index_temp = add_compute(id_temp,0);

      index_press = add_compute(id_press,0);

      index_press_scalar = add_compute(id_press,0);

      index_pe = add_compute(id_pe,0);



    } else if (strcmp(word,"evdwl") == 0) {
@@ -708,22 +723,22 @@ void Thermo::parse_fields(char *str) 


    } else if (strcmp(word,"pxx") == 0) {

      addfield("Pxx",&Thermo::compute_pxx,FLOAT);

      index_press = add_compute(id_press,1);

      index_press_vector = add_compute(id_press,1);

    } else if (strcmp(word,"pyy") == 0) {

      addfield("Pyy",&Thermo::compute_pyy,FLOAT);

      index_press = add_compute(id_press,1);

      index_press_vector = add_compute(id_press,1);

    } else if (strcmp(word,"pzz") == 0) {

      addfield("Pzz",&Thermo::compute_pzz,FLOAT);

      index_press = add_compute(id_press,1);

      index_press_vector = add_compute(id_press,1);

    } else if (strcmp(word,"pxy") == 0) {

      addfield("Pxy",&Thermo::compute_pxy,FLOAT);

      index_press = add_compute(id_press,1);

      index_press_vector = add_compute(id_press,1);

    } else if (strcmp(word,"pxz") == 0) {

      addfield("Pxz",&Thermo::compute_pxz,FLOAT);

      index_press = add_compute(id_press,1);

      index_press_vector = add_compute(id_press,1);

    } else if (strcmp(word,"pyz") == 0) {

      addfield("Pyz",&Thermo::compute_pyz,FLOAT);

      index_press = add_compute(id_press,1);

      index_press_vector = add_compute(id_press,1);



    } else if (strcmp(word,"drot") == 0) {

      addfield("RotKEdip",&Thermo::compute_drot,FLOAT);

src/thermo.h

+11 −10
Original line number Diff line number Diff line
@@ -69,14 +69,15 @@ class Thermo : protected Pointers { 
                         // internal = 1/0 if Thermo created them or not

                         // id = ID of Compute objects

                         // Compute * = ptrs to the Compute objects

  int index_temp,index_press,index_pe,index_drot,index_grot;

  int index_temp,index_press_scalar,index_press_vector,index_pe;

  int index_drot,index_grot;

  int internal_drot,internal_grot;

  char *id_temp,*id_press,*id_pe,*id_drot,*id_grot;

  class Compute *temperature,*pressure,*pe,*rotate_dipole,*rotate_gran;



  int ncompute;                // # of Compute objects called by thermo

  char **id_compute;           // their IDs

  int *compute_which;    // 0/1/2 if should call scalar() or vector() or both

  int *compute_which;          // 0/1 if should call scalar() or vector()

  class Compute **computes;    // list of ptrs to the Compute objects



  int nfix;                    // # of Fix objects called by thermo

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