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/disp,PPPMDisp)

#else

#ifndef LMP_PPPM_DISP_H
#define LMP_PPPM_DISP_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 {


#define EWALD_MAXORDER  6
#define EWALD_FUNCS     4

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

 protected:

/* ----------------------------------------------------------------------
Variables needed for calculating the 1/r and 1/r^6 potential
------------------------------------------------------------------------- */

  int function[EWALD_FUNCS];

  int me,nprocs;
  int nfactors;
  int *factors;
  double csumij;
  double csum;
  double *csumi;  //needed as correction term for per atom calculations!
  double *cii;
  int csumflag;
  double cutoff, cutoff_lj;
  double volume;
  double *B;
  double virial_1[6], virial_6[6];
  double sf_coeff[6], sf_coeff_6[6];
  int peratom_allocate_flag;

  int nsplit;
  int nsplit_alloc;

  double delxinv,delyinv,delzinv,delvolinv;
  double delxinv_6,delyinv_6,delzinv_6,delvolinv_6;

  double shift,shiftone;
  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_fft,nylo_fft,nzlo_fft,nxhi_fft,nyhi_fft,nzhi_fft;
  int nlower,nupper;
  int ngrid,nfft,nfft_both;

  double shift_6,shiftone_6;
  int nxlo_in_6,nylo_in_6,nzlo_in_6,nxhi_in_6,nyhi_in_6,nzhi_in_6;
  int nxlo_out_6,nylo_out_6,nzlo_out_6,nxhi_out_6,nyhi_out_6,nzhi_out_6;
  int nxlo_fft_6,nylo_fft_6,nzlo_fft_6,nxhi_fft_6,nyhi_fft_6,nzhi_fft_6;
  int nlower_6,nupper_6;
  int ngrid_6,nfft_6,nfft_both_6;

  //// the following variables are needed for every structure factor
  FFT_SCALAR ***density_brick;
  FFT_SCALAR ***vdx_brick,***vdy_brick,***vdz_brick;
  FFT_SCALAR *density_fft;
  FFT_SCALAR ***u_brick;
  FFT_SCALAR ***v0_brick,***v1_brick,***v2_brick,***v3_brick,***v4_brick,***v5_brick;

  FFT_SCALAR ***density_brick_g;
  FFT_SCALAR ***vdx_brick_g,***vdy_brick_g,***vdz_brick_g;
  FFT_SCALAR *density_fft_g;
  FFT_SCALAR ***u_brick_g;
  FFT_SCALAR ***v0_brick_g,***v1_brick_g,***v2_brick_g,***v3_brick_g,***v4_brick_g,***v5_brick_g;

  FFT_SCALAR ***density_brick_a0;
  FFT_SCALAR ***vdx_brick_a0,***vdy_brick_a0,***vdz_brick_a0;
  FFT_SCALAR *density_fft_a0;
  FFT_SCALAR ***u_brick_a0;
  FFT_SCALAR ***v0_brick_a0,***v1_brick_a0,***v2_brick_a0,***v3_brick_a0,***v4_brick_a0,***v5_brick_a0;

  FFT_SCALAR ***density_brick_a1;
  FFT_SCALAR ***vdx_brick_a1,***vdy_brick_a1,***vdz_brick_a1;
  FFT_SCALAR *density_fft_a1;
  FFT_SCALAR ***u_brick_a1;
  FFT_SCALAR ***v0_brick_a1,***v1_brick_a1,***v2_brick_a1,***v3_brick_a1,***v4_brick_a1,***v5_brick_a1;

  FFT_SCALAR ***density_brick_a2;
  FFT_SCALAR ***vdx_brick_a2,***vdy_brick_a2,***vdz_brick_a2;
  FFT_SCALAR *density_fft_a2;
  FFT_SCALAR ***u_brick_a2;
  FFT_SCALAR ***v0_brick_a2,***v1_brick_a2,***v2_brick_a2,***v3_brick_a2,***v4_brick_a2,***v5_brick_a2;

  FFT_SCALAR ***density_brick_a3;
  FFT_SCALAR ***vdx_brick_a3,***vdy_brick_a3,***vdz_brick_a3;
  FFT_SCALAR *density_fft_a3;
  FFT_SCALAR ***u_brick_a3;
  FFT_SCALAR ***v0_brick_a3,***v1_brick_a3,***v2_brick_a3,***v3_brick_a3,***v4_brick_a3,***v5_brick_a3;

  FFT_SCALAR ***density_brick_a4;
  FFT_SCALAR ***vdx_brick_a4,***vdy_brick_a4,***vdz_brick_a4;
  FFT_SCALAR *density_fft_a4;
  FFT_SCALAR ***u_brick_a4;
  FFT_SCALAR ***v0_brick_a4,***v1_brick_a4,***v2_brick_a4,***v3_brick_a4,***v4_brick_a4,***v5_brick_a4;

  FFT_SCALAR ***density_brick_a5;
  FFT_SCALAR ***vdx_brick_a5,***vdy_brick_a5,***vdz_brick_a5;
  FFT_SCALAR *density_fft_a5;
  FFT_SCALAR ***u_brick_a5;
  FFT_SCALAR ***v0_brick_a5,***v1_brick_a5,***v2_brick_a5,***v3_brick_a5,***v4_brick_a5,***v5_brick_a5;

  FFT_SCALAR ***density_brick_a6;
  FFT_SCALAR ***vdx_brick_a6,***vdy_brick_a6,***vdz_brick_a6;
  FFT_SCALAR *density_fft_a6;
  FFT_SCALAR ***u_brick_a6;
  FFT_SCALAR ***v0_brick_a6,***v1_brick_a6,***v2_brick_a6,***v3_brick_a6,***v4_brick_a6,***v5_brick_a6;

  FFT_SCALAR ****density_brick_none;
  FFT_SCALAR ****vdx_brick_none,****vdy_brick_none,****vdz_brick_none;
  FFT_SCALAR **density_fft_none;
  FFT_SCALAR ****u_brick_none;
  FFT_SCALAR ****v0_brick_none,****v1_brick_none,****v2_brick_none,****v3_brick_none,****v4_brick_none,****v5_brick_none;

  //// needed for each interaction type
  double *greensfn;
  double **vg;
  double **vg2;

  double *greensfn_6;
  double **vg_6;
  double **vg2_6;

  double *fkx,*fky,*fkz;
  double *fkx2, *fky2, *fkz2;
  double *fkx_6, *fky_6, *fkz_6;
  double *fkx2_6, *fky2_6, *fkz2_6;
  double *gf_b;
  double *gf_b_6;

  double *sf_precoeff1, *sf_precoeff2, *sf_precoeff3, *sf_precoeff4,
    *sf_precoeff5, *sf_precoeff6;
  double *sf_precoeff1_6, *sf_precoeff2_6, *sf_precoeff3_6,
    *sf_precoeff4_6, *sf_precoeff5_6, *sf_precoeff6_6;
  FFT_SCALAR **rho1d,**rho_coeff;
  FFT_SCALAR **drho1d, **drho_coeff;
  FFT_SCALAR **rho1d_6, **rho_coeff_6;
  FFT_SCALAR **drho1d_6, **drho_coeff_6;
  FFT_SCALAR *work1,*work2;
  FFT_SCALAR *work1_6, *work2_6;


  class FFT3d *fft1,*fft2 ;
  class FFT3d *fft1_6, *fft2_6;
  class Remap *remap;
  class Remap *remap_6;
  class GridComm *cg;
  class GridComm *cg_peratom;
  class GridComm *cg_6;
  class GridComm *cg_peratom_6;

  int **part2grid;             // storage for particle -> grid mapping
  int **part2grid_6;
  int nmax;

  int triclinic;               // domain settings, orthog or triclinic
  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

  void init_coeffs();
  int qr_alg(double**, double**, int);
  void hessenberg(double**, double**, int);
  void qr_tri(double**, double**, int);
  void mmult(double**, double**, double**, int);
  int check_convergence(double**, double**, double**,
                        double**, double**, double**, int);

  void set_grid();
  void set_grid_6();
  void set_init_g6();
  void set_fft_parameters(int&, int&, int&, int&, int&,int&,
                          int&, int&,int&, int&, int&,int&,
                          int&, int&,int&, int&, int&,int&,
                          int&, int&,int&, int&, int&,
                          int&, int&, int&,
                          double&, double&, int&);
  void set_n_pppm_6();
  void adjust_gewald();
  void adjust_gewald_6();
  double f();
  double derivf();
  double f_6();
  double derivf_6();
  double final_accuracy();
  void final_accuracy_6(double&, double&, double&);
  double lj_rspace_error();
  double compute_qopt();
  double compute_qopt_6();
  double compute_qopt_ik();
  double compute_qopt_ad();
  double compute_qopt_6_ik();
  double compute_qopt_6_ad();

  void calc_csum();

  virtual void allocate();
  virtual void allocate_peratom();
  virtual void deallocate();
  virtual void deallocate_peratom();
  int factorable(int);
  double rms(double, double, bigint, double, double **);
  double diffpr(double, double, double, double, double **);
  void compute_gf_denom(double*, int);
  double gf_denom(double, double, double, double*, int);


  void compute_sf_precoeff(int, int, int, int,
                           int, int, int,
                           int, int, int,
                           double*, double*, double*,
                           double*, double*, double*);
  void compute_gf();
  void compute_sf_coeff();
  void compute_gf_6();
  void compute_sf_coeff_6();


  virtual void particle_map(double, double, double,
                             double, int **, int, int,
                             int, int, int,
                             int, int, int);
  virtual void particle_map_c(double, double, double,
                              double, int **, int, int,
                              int, int, int,
                              int, int, int );
  virtual void make_rho_c();
  virtual void make_rho_g();
  virtual void make_rho_a();
  virtual void make_rho_none();

  virtual void brick2fft(int, int, int, int, int, int,
                         FFT_SCALAR ***, FFT_SCALAR *, FFT_SCALAR *,
                         LAMMPS_NS::Remap *);
  virtual void brick2fft_a();
  virtual void brick2fft_none();

  virtual void poisson_ik(FFT_SCALAR *, FFT_SCALAR *,
                          FFT_SCALAR *, LAMMPS_NS::FFT3d *,LAMMPS_NS::FFT3d *,
                          int, int, int, int, int, int, int,
                          int, int, int, int, int, int,
                          int, int, int, double&, double *,
                          double *, double *, double *,
                          double *, double *, double *,
                          FFT_SCALAR ***, FFT_SCALAR ***, FFT_SCALAR ***, double *, double **, double **,
                          FFT_SCALAR ***, FFT_SCALAR ***, FFT_SCALAR ***, FFT_SCALAR ***,
                          FFT_SCALAR ***, FFT_SCALAR ***, FFT_SCALAR ***);

  virtual void poisson_ad(FFT_SCALAR*, FFT_SCALAR*,
                          FFT_SCALAR*, LAMMPS_NS::FFT3d*,LAMMPS_NS::FFT3d*,
                          int, int, int, int,
                          int, int, int, int, int, int,
                          int, int, int, int, int, int,
                          double&, double*,
                          double*, double**, double**,
                          FFT_SCALAR***, FFT_SCALAR***, FFT_SCALAR***, FFT_SCALAR***,
                          FFT_SCALAR***, FFT_SCALAR***, FFT_SCALAR***);

  virtual void poisson_peratom(FFT_SCALAR*, FFT_SCALAR*, LAMMPS_NS::FFT3d*,
                               double**, double**, int,
                               int, int, int, int, int, int,
                               FFT_SCALAR***, FFT_SCALAR***, FFT_SCALAR***,
                               FFT_SCALAR***, FFT_SCALAR***, FFT_SCALAR***);
  virtual void poisson_2s_ik(FFT_SCALAR *, FFT_SCALAR *,
                             FFT_SCALAR ***, FFT_SCALAR ***, FFT_SCALAR ***,
                             FFT_SCALAR ***, FFT_SCALAR ***, FFT_SCALAR ***,
                             FFT_SCALAR ***, FFT_SCALAR ***, FFT_SCALAR ***, FFT_SCALAR ***,
                             FFT_SCALAR ***, FFT_SCALAR ***, FFT_SCALAR ***,
                             FFT_SCALAR ***, FFT_SCALAR ***, FFT_SCALAR ***, FFT_SCALAR ***,
                             FFT_SCALAR ***, FFT_SCALAR ***, FFT_SCALAR ***);
  virtual void poisson_2s_ad(FFT_SCALAR *, FFT_SCALAR *,
                             FFT_SCALAR ***, FFT_SCALAR ***, FFT_SCALAR ***, FFT_SCALAR ***,
                             FFT_SCALAR ***, FFT_SCALAR ***, FFT_SCALAR ***,
                             FFT_SCALAR ***, FFT_SCALAR ***, FFT_SCALAR ***, FFT_SCALAR ***,
                             FFT_SCALAR ***, FFT_SCALAR ***, FFT_SCALAR ***);

  virtual void poisson_2s_peratom(FFT_SCALAR***, FFT_SCALAR***, FFT_SCALAR***,
                                  FFT_SCALAR***, FFT_SCALAR***, FFT_SCALAR***,
                                  FFT_SCALAR***, FFT_SCALAR***, FFT_SCALAR***,
                                  FFT_SCALAR***, FFT_SCALAR***, FFT_SCALAR***);

  virtual void poisson_none_ad(int, int, FFT_SCALAR *, FFT_SCALAR *,
                               FFT_SCALAR ***, FFT_SCALAR ***,
                               FFT_SCALAR ****, FFT_SCALAR ****, FFT_SCALAR ****,
                               FFT_SCALAR ****, FFT_SCALAR ****, FFT_SCALAR ****);
  virtual void poisson_none_ik(int, int, FFT_SCALAR *, FFT_SCALAR *,
                               FFT_SCALAR ***, FFT_SCALAR ***, FFT_SCALAR ***,
                               FFT_SCALAR ***, FFT_SCALAR ***, FFT_SCALAR ***,
                               FFT_SCALAR ****, FFT_SCALAR ****, FFT_SCALAR ****, FFT_SCALAR ****,
                               FFT_SCALAR ****, FFT_SCALAR ****, FFT_SCALAR ****);
  virtual void poisson_none_peratom(int, int, FFT_SCALAR***, FFT_SCALAR***, FFT_SCALAR***,
                                    FFT_SCALAR***, FFT_SCALAR***, FFT_SCALAR***,
                                    FFT_SCALAR***, FFT_SCALAR***, FFT_SCALAR***,
                                    FFT_SCALAR***, FFT_SCALAR***, FFT_SCALAR***);


  virtual void fieldforce_c_ik();
  virtual void fieldforce_c_ad();
  virtual void fieldforce_c_peratom();
  virtual void fieldforce_g_ik();
  virtual void fieldforce_g_ad();
  virtual void fieldforce_g_peratom();
  virtual void fieldforce_a_ik();
  virtual void fieldforce_a_ad();
  virtual void fieldforce_a_peratom();
  virtual void fieldforce_none_ik();
  virtual void fieldforce_none_ad();
  virtual void fieldforce_none_peratom();
  void procs2grid2d(int,int,int,int *, int*);
  void compute_rho1d(const FFT_SCALAR &, const FFT_SCALAR &,
                     const FFT_SCALAR &, int, FFT_SCALAR **, FFT_SCALAR **);
  void compute_drho1d(const FFT_SCALAR &, const FFT_SCALAR &,
                      const FFT_SCALAR &, int, FFT_SCALAR **, FFT_SCALAR **);
  void compute_rho_coeff(FFT_SCALAR **,FFT_SCALAR **, int);
  void slabcorr(int);

  // grid communication

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

}

#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: Cannot use PPPMDisp with 2d simulation

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

E: PPPMDisp can only currently be used with comm_style brick

This is a current restriction in LAMMPS.

E: Cannot use non-periodic boundaries with PPPMDisp

For kspace style pppm/disp, 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 PPPMDisp

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

E: PPPMDisp coulomb order cannot be greater 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: Unsupported order in kspace_style pppm/disp, pair_style %s

Only pair styles with 1/r and 1/r^6 dependence are currently supported.

W: Charges are set, but coulombic solver is not used

Self-explanatory.

E: PPPMDisp used but no parameters set, for further information please see the pppm/disp documentation

An efficient and accurate usage of the pppm/disp requires settings via the kspace_modify command. Please see the pppm/disp documentation for further instructions.

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 PPPMDisp/TIP4P

Specified angle type is not valid.

E: Bad TIP4P bond type for PPPMDisp/TIP4P

Specified bond type is not valid.

W: Reducing PPPMDisp Coulomb order b/c stencil extends beyond 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: PPPMDisp Coulomb 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: Coulomb PPPMDisp order has been reduced below minorder

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

W: Reducing PPPMDisp dispersion order b/c stencil extends beyond 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: PPPMDisp Dispersion 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: Dispersion PPPMDisp order has been reduced below minorder

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: Matrix factorization to split dispersion coefficients failed

This should not normally happen.  Contact the developers.

W: Estimated error in splitting of dispersion coeffs is %g

Error is greater than 0.0001 percent.

W: Simulations might be very slow because of large number of structure factors

Self-explanatory.

E: Epsilon or sigma reference not set by pair style in PPPMDisp

Self-explanatory.

E: KSpace accuracy too large to estimate G vector

Reduce the accuracy request or specify gewald explicitly
via the kspace_modify command.

E: Could not compute grid size for Coulomb interaction

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: 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: Could not adjust g_ewald_6

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: Cannot compute initial g_ewald_disp

LAMMPS failed to compute an initial guess for the PPPM_disp g_ewald_6
factor that partitions the computation between real space and k-space
for Dispersion interactions.

E: Could not compute grid size for Dispersion

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: Non-numeric box dimensions - simulation unstable

The box size has apparently blown up.

E: Out of range atoms - cannot compute PPPMDisp

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.

*/