Commit ae5764be authored by Steve Plimpton's avatar Steve Plimpton
Browse files

added functionity to lib interface

parent fb3f597f

doc/src/Section_howto.txt

+22 −9
Original line number Diff line number Diff line
@@ -1936,18 +1936,22 @@ documentation in the src/library.cpp file for details, including 
which quantities can be queried by name:



void *lammps_extract_global(void *, char *)

void lammps_extract_box(void *, double *, double *, 

                        double *, double *, double *, int *, int *)

void *lammps_extract_atom(void *, char *)

void *lammps_extract_compute(void *, char *, int, int)

void *lammps_extract_fix(void *, char *, int, int, int, int)

void *lammps_extract_variable(void *, char *, char *) :pre



int lammps_set_variable(void *, char *, char *)

double lammps_get_thermo(void *, char *) :pre

void lammps_reset_box(void *, double *, double *, double, double, double)

int lammps_set_variable(void *, char *, char *) :pre



double lammps_get_thermo(void *, char *)

int lammps_get_natoms(void *)

void lammps_gather_atoms(void *, double *)

void lammps_scatter_atoms(void *, double *) :pre

void lammps_create_atoms(void *, int, tagint *, int *, double *, double *) :pre

void lammps_create_atoms(void *, int, tagint *, int *, double *, double *,

                         imageint *, int) :pre



The extract functions return a pointer to various global or per-atom

quantities stored in LAMMPS or to values calculated by a compute, fix,
@@ -1957,10 +1961,16 @@ the other extract functions, the underlying storage may be reallocated 
as LAMMPS runs, so you need to re-call the function to assure a

current pointer or returned value(s).



The lammps_reset_box() function resets the size and shape of the

simulation box, e.g. as part of restoring a previously extracted and

saved state of a simulation.



The lammps_set_variable() function can set an existing string-style

variable to a new string value, so that subsequent LAMMPS commands can

access the variable.  The lammps_get_thermo() function returns the

current value of a thermo keyword as a double.

access the variable.



The lammps_get_thermo() function returns the current value of a thermo

keyword as a double precision value.



The lammps_get_natoms() function returns the total number of atoms in

the system and can be used by the caller to allocate space for the
@@ -1973,10 +1983,13 @@ passed by the caller, to each atom owned by individual processors. 


The lammps_create_atoms() function takes a list of N atoms as input

with atom types and coords (required), an optionally atom IDs and

velocities.  It uses the coords of each atom to assign it as a new

atom to the processor that owns it.  Additional properties for the new

atoms can be assigned via the lammps_scatter_atoms() or

lammps_extract_atom() functions.

velocities and image flags.  It uses the coords of each atom to assign

it as a new atom to the processor that owns it.  This function is

useful to add atoms to a simulation or (in tandem with

lammps_reset_box()) to restore a previously extracted and saved state

of a simulation.  Additional properties for the new atoms can then be

assigned via the lammps_scatter_atoms() or lammps_extract_atom()

functions.



The examples/COUPLE and python directories have example C++ and C and

Python codes which show how a driver code can link to LAMMPS as a

src/KSPACE/ewald_disp.cpp

+12 −12
Original line number Diff line number Diff line
@@ -195,23 +195,22 @@ void EwaldDisp::init() 
      g_ewald = accuracy*sqrt(natoms*(*cutoff)*shape_det(domain->h)) / (2.0*q2);

      if (g_ewald >= 1.0) g_ewald = (1.35 - 0.15*log(accuracy))/(*cutoff);

      else g_ewald = sqrt(-log(g_ewald)) / (*cutoff);

    }

    else if (function[1] || function[2]) {

    } else if (function[3]) {

      //Try Newton Solver

      //Use old method to get guess

      g_ewald = (1.35 - 0.15*log(accuracy))/ *cutoff;



      double g_ewald_new =

        NewtonSolve(g_ewald,(*cutoff),natoms,shape_det(domain->h),b2);

        NewtonSolve(g_ewald,(*cutoff),natoms,shape_det(domain->h),M2);

      if (g_ewald_new > 0.0) g_ewald = g_ewald_new;

      else error->warning(FLERR,"Ewald/disp Newton solver failed, "

                          "using old method to estimate g_ewald");

    } else if (function[3]) {

    } else if (function[1] || function[2]) {

      //Try Newton Solver

      //Use old method to get guess

      g_ewald = (1.35 - 0.15*log(accuracy))/ *cutoff;



      double g_ewald_new =

        NewtonSolve(g_ewald,(*cutoff),natoms,shape_det(domain->h),M2);

        NewtonSolve(g_ewald,(*cutoff),natoms,shape_det(domain->h),b2);

      if (g_ewald_new > 0.0) g_ewald = g_ewald_new;

      else error->warning(FLERR,"Ewald/disp Newton solver failed, "

                          "using old method to estimate g_ewald");
@@ -708,6 +707,8 @@ void EwaldDisp::compute(int eflag, int vflag) 
  compute_virial();

  compute_virial_dipole();

  compute_virial_peratom();



  if (slabflag) compute_slabcorr();

}
@@ -974,7 +975,6 @@ void EwaldDisp::compute_energy() 
    }

  }

  for (int k=0; k<EWALD_NFUNCS; ++k) energy += c[k]*sum[k]-energy_self[k];

  if (slabflag) compute_slabcorr();

}



/* ---------------------------------------------------------------------- */
@@ -1480,10 +1480,7 @@ double EwaldDisp::f(double x, double Rc, bigint natoms, double vol, double b2) 
  double a = Rc*x;

  double f = 0.0;



  if (function[1] || function[2]) { // LJ

    f = (4.0*MY_PI*b2*powint(x,4)/vol/sqrt((double)natoms)*erfc(a) *

      (6.0*powint(a,-5) + 6.0*powint(a,-3) + 3.0/a + a) - accuracy);

  } else { // dipole

  if (function[3]) { // dipole

    double rg2 = a*a;

    double rg4 = rg2*rg2;

    double rg6 = rg4*rg2;
@@ -1492,6 +1489,9 @@ double EwaldDisp::f(double x, double Rc, bigint natoms, double vol, double b2) 
    f = (b2/(sqrt(vol*powint(x,4)*powint(Rc,9)*natoms)) *

      sqrt(13.0/6.0*Cc*Cc + 2.0/15.0*Dc*Dc - 13.0/15.0*Cc*Dc) *

      exp(-rg2)) - accuracy;

  } else if (function[1] || function[2]) { // LJ

    f = (4.0*MY_PI*b2*powint(x,4)/vol/sqrt((double)natoms)*erfc(a) *

      (6.0*powint(a,-5) + 6.0*powint(a,-3) + 3.0/a + a) - accuracy);

  }



  return f;

src/REPLICA/prd.cpp

+1 −0
Original line number Diff line number Diff line
@@ -241,6 +241,7 @@ void PRD::command(int narg, char **arg) 
  update->minimize->init();



  // cannot use PRD with a changing box

  // removing this restriction would require saving/restoring box params



  if (domain->box_change)

    error->all(FLERR,"Cannot use PRD with a changing box");

src/RIGID/compute_rigid_local.cpp

+15 −14
Original line number Diff line number Diff line
@@ -33,7 +33,8 @@ enum{ID,MOL,MASS,X,Y,Z,XU,YU,ZU,VX,VY,VZ,FX,FY,FZ,IX,IY,IZ, 
/* ---------------------------------------------------------------------- */



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

  Compute(lmp, narg, arg), rstyle(NULL), idrigid(NULL), fixrigid(NULL)

  Compute(lmp, narg, arg), 

  rstyle(NULL), idrigid(NULL), fixrigid(NULL), vlocal(NULL), alocal(NULL)

{

  if (narg < 5) error->all(FLERR,"Illegal compute rigid/local command");
@@ -88,16 +89,16 @@ ComputeRigidLocal::ComputeRigidLocal(LAMMPS *lmp, int narg, char **arg) : 
  }



  ncount = nmax = 0;

  vector = NULL;

  array = NULL;

  vlocal = NULL;

  alocal = NULL;

}



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



ComputeRigidLocal::~ComputeRigidLocal()

{

  memory->destroy(vector);

  memory->destroy(array);

  memory->destroy(vlocal);

  memory->destroy(alocal);

  delete [] idrigid;

  delete [] rstyle;

}
@@ -169,8 +170,8 @@ int ComputeRigidLocal::compute_rigid(int flag) 
    body = &fixrigid->body[ibody];



    if (flag) {

      if (nvalues == 1) ptr = &vector[m];

      else ptr = array[m];

      if (nvalues == 1) ptr = &vlocal[m];

      else ptr = alocal[m];



      for (n = 0; n < nvalues; n++) {

        switch (rstyle[n]) {
@@ -293,18 +294,18 @@ int ComputeRigidLocal::compute_rigid(int flag) 


void ComputeRigidLocal::reallocate(int n)

{

  // grow vector or array

  // grow vector_local or array_local



  while (nmax < n) nmax += DELTA;



  if (nvalues == 1) {

    memory->destroy(vector);

    memory->create(vector,nmax,"rigid/local:vector");

    vector_local = vector;

    memory->destroy(vlocal);

    memory->create(vlocal,nmax,"rigid/local:vector_local");

    vector_local = vlocal;

  } else {

    memory->destroy(array);

    memory->create(array,nmax,nvalues,"rigid/local:array");

    array_local = array;

    memory->destroy(alocal);

    memory->create(alocal,nmax,nvalues,"rigid/local:array_local");

    array_local = alocal;

  }

}

src/RIGID/compute_rigid_local.h

+2 −0
Original line number Diff line number Diff line
@@ -41,6 +41,8 @@ class ComputeRigidLocal : public Compute { 
  class FixRigidSmall *fixrigid;



  int nmax;

  double *vlocal;

  double **alocal;



  int compute_rigid(int);

  void reallocate(int);

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