lammps-sys 0.6.0

/* -*- c++ -*- ----------------------------------------------------------
   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
   http://lammps.sandia.gov, Sandia National Laboratories
   Steve Plimpton, sjplimp@sandia.gov

   Copyright (2003) Sandia Corporation.  Under the terms of Contract
   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
   certain rights in this software.  This software is distributed under
   the GNU General Public License.

   See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */

#ifdef KSPACE_CLASS

KSpaceStyle(pppm,PPPM)

#else

#ifndef LMP_PPPM_H
#define LMP_PPPM_H

#include "kspace.h"

#if defined(FFT_FFTW3)
#define LMP_FFT_LIB "FFTW3"
#elif defined(FFT_MKL)
#define LMP_FFT_LIB "MKL FFT"
#else
#define LMP_FFT_LIB "KISS FFT"
#endif

#ifdef FFT_SINGLE
typedef float FFT_SCALAR;
#define LMP_FFT_PREC "single"
#define MPI_FFT_SCALAR MPI_FLOAT
#else

typedef double FFT_SCALAR;
#define LMP_FFT_PREC "double"
#define MPI_FFT_SCALAR MPI_DOUBLE
#endif

namespace LAMMPS_NS {

class PPPM : public KSpace {
 public:
  PPPM(class LAMMPS *);
  virtual ~PPPM();
  virtual void settings(int, char **);
  virtual void init();
  virtual void setup();
  virtual void setup_grid();
  virtual void compute(int, int);
  virtual int timing_1d(int, double &);
  virtual int timing_3d(int, double &);
  virtual double memory_usage();

  virtual void compute_group_group(int, int, int);

 protected:
  int me,nprocs;
  int nfactors;
  int *factors;
  double cutoff;
  double volume;
  double delxinv,delyinv,delzinv,delvolinv;
  double h_x,h_y,h_z;
  double shift,shiftone;
  int peratom_allocate_flag;

  int nxlo_in,nylo_in,nzlo_in,nxhi_in,nyhi_in,nzhi_in;
  int nxlo_out,nylo_out,nzlo_out,nxhi_out,nyhi_out,nzhi_out;
  int nxlo_ghost,nxhi_ghost,nylo_ghost,nyhi_ghost,nzlo_ghost,nzhi_ghost;
  int nxlo_fft,nylo_fft,nzlo_fft,nxhi_fft,nyhi_fft,nzhi_fft;
  int nlower,nupper;
  int ngrid,nfft,nfft_both;

  FFT_SCALAR ***density_brick;
  FFT_SCALAR ***vdx_brick,***vdy_brick,***vdz_brick;
  FFT_SCALAR ***u_brick;
  FFT_SCALAR ***v0_brick,***v1_brick,***v2_brick;
  FFT_SCALAR ***v3_brick,***v4_brick,***v5_brick;
  double *greensfn;
  double **vg;
  double *fkx,*fky,*fkz;
  FFT_SCALAR *density_fft;
  FFT_SCALAR *work1,*work2;

  double *gf_b;
  FFT_SCALAR **rho1d,**rho_coeff,**drho1d,**drho_coeff;
  double *sf_precoeff1, *sf_precoeff2, *sf_precoeff3;
  double *sf_precoeff4, *sf_precoeff5, *sf_precoeff6;
  double sf_coeff[6];          // coefficients for calculating ad self-forces
  double **acons;

  // group-group interactions

  int group_allocate_flag;
  FFT_SCALAR ***density_A_brick,***density_B_brick;
  FFT_SCALAR *density_A_fft,*density_B_fft;

  class FFT3d *fft1,*fft2;
  class Remap *remap;
  class GridComm *cg;
  class GridComm *cg_peratom;

  int **part2grid;             // storage for particle -> grid mapping
  int nmax;

  double *boxlo;
                               // TIP4P settings
  int typeH,typeO;             // atom types of TIP4P water H and O atoms
  double qdist;                // distance from O site to negative charge
  double alpha;                // geometric factor

  virtual void set_grid_global();
  void set_grid_local();
  void adjust_gewald();
  virtual double newton_raphson_f();
  double derivf();
  double final_accuracy();

  virtual void allocate();
  virtual void allocate_peratom();
  virtual void deallocate();
  virtual void deallocate_peratom();
  int factorable(int);
  double compute_df_kspace();
  double estimate_ik_error(double, double, bigint);
  virtual double compute_qopt();
  virtual void compute_gf_denom();
  virtual void compute_gf_ik();
  virtual void compute_gf_ad();
  void compute_sf_precoeff();

  virtual void particle_map();
  virtual void make_rho();
  virtual void brick2fft();

  virtual void poisson();
  virtual void poisson_ik();
  virtual void poisson_ad();

  virtual void fieldforce();
  virtual void fieldforce_ik();
  virtual void fieldforce_ad();

  virtual void poisson_peratom();
  virtual void fieldforce_peratom();
  void procs2grid2d(int,int,int,int *, int*);
  void compute_rho1d(const FFT_SCALAR &, const FFT_SCALAR &,
                     const FFT_SCALAR &);
  void compute_drho1d(const FFT_SCALAR &, const FFT_SCALAR &,
                     const FFT_SCALAR &);
  void compute_rho_coeff();
  virtual void slabcorr();

  // grid communication

  virtual void pack_forward(int, FFT_SCALAR *, int, int *);
  virtual void unpack_forward(int, FFT_SCALAR *, int, int *);
  virtual void pack_reverse(int, FFT_SCALAR *, int, int *);
  virtual void unpack_reverse(int, FFT_SCALAR *, int, int *);

  // triclinic

  int triclinic;               // domain settings, orthog or triclinic
  void setup_triclinic();
  void compute_gf_ik_triclinic();
  void poisson_ik_triclinic();
  void poisson_groups_triclinic();

  // group-group interactions

  virtual void allocate_groups();
  virtual void deallocate_groups();
  virtual void make_rho_groups(int, int, int);
  virtual void poisson_groups(int);
  virtual void slabcorr_groups(int,int,int);

/* ----------------------------------------------------------------------
   denominator for Hockney-Eastwood Green's function
     of x,y,z = sin(kx*deltax/2), etc

            inf                 n-1
   S(n,k) = Sum  W(k+pi*j)**2 = Sum b(l)*(z*z)**l
           j=-inf               l=0

          = -(z*z)**n /(2n-1)! * (d/dx)**(2n-1) cot(x)  at z = sin(x)
   gf_b = denominator expansion coeffs
------------------------------------------------------------------------- */

  inline double gf_denom(const double &x, const double &y,
                         const double &z) const {
    double sx,sy,sz;
    sz = sy = sx = 0.0;
    for (int l = order-1; l >= 0; l--) {
      sx = gf_b[l] + sx*x;
      sy = gf_b[l] + sy*y;
      sz = gf_b[l] + sz*z;
    }
    double s = sx*sy*sz;
    return s*s;
  };
};

}

#endif
#endif

/* ERROR/WARNING messages:

E: Illegal ... command

Self-explanatory.  Check the input script syntax and compare to the
documentation for the command.  You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.

E: Must redefine kspace_style after changing to triclinic box

UNDOCUMENTED

E: Cannot (yet) use PPPM with triclinic box and kspace_modify diff ad

This feature is not yet supported.

E: Cannot (yet) use PPPM with triclinic box and slab correction

This feature is not yet supported.

E: Cannot use PPPM with 2d simulation

The kspace style pppm cannot be used in 2d simulations.  You can use
2d PPPM in a 3d simulation; see the kspace_modify command.

E: PPPM can only currently be used with comm_style brick

This is a current restriction in LAMMPS.

E: Kspace style requires atom attribute q

The atom style defined does not have these attributes.

E: Cannot use non-periodic boundaries with PPPM

For kspace style pppm, all 3 dimensions must have periodic boundaries
unless you use the kspace_modify command to define a 2d slab with a
non-periodic z dimension.

E: Incorrect boundaries with slab PPPM

Must have periodic x,y dimensions and non-periodic z dimension to use
2d slab option with PPPM.

E: PPPM order cannot be < 2 or > than %d

This is a limitation of the PPPM implementation in LAMMPS.

E: KSpace style is incompatible with Pair style

Setting a kspace style requires that a pair style with matching
long-range Coulombic or dispersion components be used.

E: Pair style is incompatible with TIP4P KSpace style

The pair style does not have the requires TIP4P settings.

E: Bond and angle potentials must be defined for TIP4P

Cannot use TIP4P pair potential unless bond and angle potentials
are defined.

E: Bad TIP4P angle type for PPPM/TIP4P

Specified angle type is not valid.

E: Bad TIP4P bond type for PPPM/TIP4P

Specified bond type is not valid.

W: Reducing PPPM order b/c stencil extends beyond nearest neighbor processor

This may lead to a larger grid than desired.  See the kspace_modify overlap
command to prevent changing of the PPPM order.

E: PPPM order < minimum allowed order

The default minimum order is 2.  This can be reset by the
kspace_modify minorder command.

E: PPPM grid stencil extends beyond nearest neighbor processor

This is not allowed if the kspace_modify overlap setting is no.

E: KSpace accuracy must be > 0

The kspace accuracy designated in the input must be greater than zero.

E: Must use kspace_modify gewald for uncharged system

UNDOCUMENTED

E: Could not compute grid size

The code is unable to compute a grid size consistent with the desired
accuracy.  This error should not occur for typical problems.  Please
send an email to the developers.

E: PPPM grid is too large

The global PPPM grid is larger than OFFSET in one or more dimensions.
OFFSET is currently set to 4096.  You likely need to decrease the
requested accuracy.

E: Could not compute g_ewald

The Newton-Raphson solver failed to converge to a good value for
g_ewald.  This error should not occur for typical problems.  Please
send an email to the developers.

E: Non-numeric box dimensions - simulation unstable

The box size has apparently blown up.

E: Out of range atoms - cannot compute PPPM

One or more atoms are attempting to map their charge to a PPPM grid
point that is not owned by a processor.  This is likely for one of two
reasons, both of them bad.  First, it may mean that an atom near the
boundary of a processor's sub-domain has moved more than 1/2 the
"neighbor skin distance"_neighbor.html without neighbor lists being
rebuilt and atoms being migrated to new processors.  This also means
you may be missing pairwise interactions that need to be computed.
The solution is to change the re-neighboring criteria via the
"neigh_modify"_neigh_modify command.  The safest settings are "delay 0
every 1 check yes".  Second, it may mean that an atom has moved far
outside a processor's sub-domain or even the entire simulation box.
This indicates bad physics, e.g. due to highly overlapping atoms, too
large a timestep, etc.

E: Cannot (yet) use K-space slab correction with compute group/group for triclinic systems

This option is not yet supported.

E: Cannot (yet) use kspace_modify diff ad with compute group/group

This option is not yet supported.

U: Cannot (yet) use PPPM with triclinic box and TIP4P

This feature is not yet supported.

*/