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src/KSPACE/pppm.cpp
6792
src/KSPACE/pppm.cpp
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/* -*- c++ -*- ----------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#ifdef KSPACE_CLASS
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KSpaceStyle(pppm,PPPM)
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#else
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#ifndef LMP_PPPM_H
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#define LMP_PPPM_H
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#include "lmptype.h"
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#include "mpi.h"
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#ifdef FFT_SINGLE
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typedef float FFT_SCALAR;
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#define MPI_FFT_SCALAR MPI_FLOAT
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#else
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typedef double FFT_SCALAR;
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#define MPI_FFT_SCALAR MPI_DOUBLE
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#endif
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#include "kspace.h"
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namespace LAMMPS_NS {
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class PPPM : public KSpace {
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public:
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PPPM(class LAMMPS *, int, char **);
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virtual ~PPPM();
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virtual void init();
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virtual void setup();
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void setup_grid();
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virtual void compute(int, int);
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virtual int timing_1d(int, double &);
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virtual int timing_3d(int, double &);
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virtual double memory_usage();
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virtual void compute_group_group(int, int, int);
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protected:
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int me,nprocs;
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int nfactors;
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int *factors;
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double qsum,qsqsum,q2;
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double cutoff;
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double volume;
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double delxinv,delyinv,delzinv,delvolinv;
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double h_x,h_y,h_z;
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double shift,shiftone;
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int peratom_allocate_flag;
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int nxlo_in,nylo_in,nzlo_in,nxhi_in,nyhi_in,nzhi_in;
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int nxlo_out,nylo_out,nzlo_out,nxhi_out,nyhi_out,nzhi_out;
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int nxlo_ghost,nxhi_ghost,nylo_ghost,nyhi_ghost,nzlo_ghost,nzhi_ghost;
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int nxlo_fft,nylo_fft,nzlo_fft,nxhi_fft,nyhi_fft,nzhi_fft;
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int nlower,nupper;
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int ngrid,nfft,nfft_both;
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FFT_SCALAR ***density_brick;
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FFT_SCALAR ***vdx_brick,***vdy_brick,***vdz_brick;
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FFT_SCALAR ***u_brick;
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FFT_SCALAR ***v0_brick,***v1_brick,***v2_brick;
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FFT_SCALAR ***v3_brick,***v4_brick,***v5_brick;
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double *greensfn;
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double **vg;
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double *fkx,*fky,*fkz;
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FFT_SCALAR *density_fft;
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FFT_SCALAR *work1,*work2;
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double *gf_b;
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FFT_SCALAR **rho1d,**rho_coeff,**drho1d,**drho_coeff;
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double *sf_precoeff1, *sf_precoeff2, *sf_precoeff3;
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double *sf_precoeff4, *sf_precoeff5, *sf_precoeff6;
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double sf_coeff[6]; // coefficients for calculating ad self-forces
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double **acons;
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// group-group interactions
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int group_allocate_flag;
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FFT_SCALAR ***density_A_brick,***density_B_brick;
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FFT_SCALAR *density_A_fft,*density_B_fft;
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class FFT3d *fft1,*fft2;
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class Remap *remap;
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class CommGrid *cg;
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class CommGrid *cg_peratom;
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int **part2grid; // storage for particle -> grid mapping
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int nmax;
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double *boxlo;
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// TIP4P settings
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int typeH,typeO; // atom types of TIP4P water H and O atoms
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double qdist; // distance from O site to negative charge
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double alpha; // geometric factor
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void set_grid_global();
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void set_grid_local();
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void adjust_gewald();
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double newton_raphson_f();
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double derivf();
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double final_accuracy();
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virtual void allocate();
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virtual void allocate_peratom();
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virtual void deallocate();
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virtual void deallocate_peratom();
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int factorable(int);
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double compute_df_kspace();
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double estimate_ik_error(double, double, bigint);
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virtual double compute_qopt();
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virtual void compute_gf_denom();
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virtual void compute_gf_ik();
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virtual void compute_gf_ad();
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void compute_sf_precoeff();
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virtual void particle_map();
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virtual void make_rho();
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virtual void brick2fft();
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virtual void poisson();
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virtual void poisson_ik();
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virtual void poisson_ad();
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virtual void fieldforce();
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virtual void fieldforce_ik();
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virtual void fieldforce_ad();
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virtual void poisson_peratom();
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virtual void fieldforce_peratom();
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void procs2grid2d(int,int,int,int *, int*);
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void compute_rho1d(const FFT_SCALAR &, const FFT_SCALAR &,
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const FFT_SCALAR &);
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void compute_drho1d(const FFT_SCALAR &, const FFT_SCALAR &,
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const FFT_SCALAR &);
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void compute_rho_coeff();
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void slabcorr();
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// grid communication
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virtual void pack_forward(int, FFT_SCALAR *, int, int *);
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virtual void unpack_forward(int, FFT_SCALAR *, int, int *);
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virtual void pack_reverse(int, FFT_SCALAR *, int, int *);
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virtual void unpack_reverse(int, FFT_SCALAR *, int, int *);
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// triclinic
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int triclinic; // domain settings, orthog or triclinic
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void setup_triclinic();
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void compute_gf_ik_triclinic();
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void poisson_ik_triclinic();
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void poisson_groups_triclinic();
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// group-group interactions
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virtual void allocate_groups();
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virtual void deallocate_groups();
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virtual void make_rho_groups(int, int, int);
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virtual void poisson_groups(int);
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/* ----------------------------------------------------------------------
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denominator for Hockney-Eastwood Green's function
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of x,y,z = sin(kx*deltax/2), etc
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inf n-1
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S(n,k) = Sum W(k+pi*j)**2 = Sum b(l)*(z*z)**l
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j=-inf l=0
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= -(z*z)**n /(2n-1)! * (d/dx)**(2n-1) cot(x) at z = sin(x)
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gf_b = denominator expansion coeffs
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------------------------------------------------------------------------- */
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inline double gf_denom(const double &x, const double &y,
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const double &z) const {
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double sx,sy,sz;
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sz = sy = sx = 0.0;
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for (int l = order-1; l >= 0; l--) {
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sx = gf_b[l] + sx*x;
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sy = gf_b[l] + sy*y;
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sz = gf_b[l] + sz*z;
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}
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double s = sx*sy*sz;
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return s*s;
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};
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};
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}
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#endif
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#endif
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/* ERROR/WARNING messages:
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E: Illegal ... command
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Self-explanatory. Check the input script syntax and compare to the
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documentation for the command. You can use -echo screen as a
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command-line option when running LAMMPS to see the offending line.
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E: Cannot (yet) use PPPM with triclinic box and 'kspace_modify diff ad'
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This feature is not yet supported.
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E: Cannot (yet) use PPPM with triclinic box and slab correction
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This feature is not yet supported.
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E: Cannot use PPPM with 2d simulation
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The kspace style pppm cannot be used in 2d simulations. You can use
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2d PPPM in a 3d simulation; see the kspace_modify command.
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E: Kspace style requires atom attribute q
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The atom style defined does not have these attributes.
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E: Cannot use nonperiodic boundaries with PPPM
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For kspace style pppm, all 3 dimensions must have periodic boundaries
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unless you use the kspace_modify command to define a 2d slab with a
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non-periodic z dimension.
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E: Incorrect boundaries with slab PPPM
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Must have periodic x,y dimensions and non-periodic z dimension to use
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2d slab option with PPPM.
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E: PPPM order cannot be < 2 or > than %d
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This is a limitation of the PPPM implementation in LAMMPS.
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E: KSpace style is incompatible with Pair style
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Setting a kspace style requires that a pair style with a long-range
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Coulombic or dispersion component be used.
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E: Bond and angle potentials must be defined for TIP4P
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Cannot use TIP4P pair potential unless bond and angle potentials
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are defined.
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E: Bad TIP4P angle type for PPPM/TIP4P
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Specified angle type is not valid.
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E: Bad TIP4P bond type for PPPM/TIP4P
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Specified bond type is not valid.
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E: Cannot (yet) use PPPM with triclinic box and TIP4P
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This feature is not yet supported.
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E: Cannot use kspace solver on system with no charge
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No atoms in system have a non-zero charge.
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W: System is not charge neutral, net charge = %g
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The total charge on all atoms on the system is not 0.0, which
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is not valid for the long-range Coulombic solvers.
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W: Reducing PPPM order b/c stencil extends beyond nearest neighbor processor
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This may lead to a larger grid than desired. See the kspace_modify overlap
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command to prevent changing of the PPPM order.
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E: PPPM order < minimum allowed order
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The default minimum order is 2. This can be reset by the
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kspace_modify minorder command.
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E: PPPM grid stencil extends beyond nearest neighbor processor
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This is not allowed if the kspace_modify overlap setting is no.
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E: KSpace accuracy must be > 0
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The kspace accuracy designated in the input must be greater than zero.
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E: Could not compute grid size
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The code is unable to compute a grid size consistent with the desired
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accuracy. This error should not occur for typical problems. Please
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send an email to the developers.
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E: PPPM grid is too large
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The global PPPM grid is larger than OFFSET in one or more dimensions.
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OFFSET is currently set to 4096. You likely need to decrease the
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requested accuracy.
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E: Could not compute g_ewald
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The Newton-Raphson solver failed to converge to a good value for
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g_ewald. This error should not occur for typical problems. Please
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send an email to the developers.
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E: Out of range atoms - cannot compute PPPM
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One or more atoms are attempting to map their charge to a PPPM grid
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point that is not owned by a processor. This is likely for one of two
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reasons, both of them bad. First, it may mean that an atom near the
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boundary of a processor's sub-domain has moved more than 1/2 the
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"neighbor skin distance"_neighbor.html without neighbor lists being
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rebuilt and atoms being migrated to new processors. This also means
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you may be missing pairwise interactions that need to be computed.
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The solution is to change the re-neighboring criteria via the
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"neigh_modify"_neigh_modify command. The safest settings are "delay 0
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every 1 check yes". Second, it may mean that an atom has moved far
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outside a processor's sub-domain or even the entire simulation box.
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This indicates bad physics, e.g. due to highly overlapping atoms, too
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large a timestep, etc.
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E: Cannot (yet) use K-space slab correction with compute group/group
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This option is not yet supported.
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E: Cannot (yet) use 'kspace_modify diff ad' with compute group/group
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This option is not yet supported.
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*/
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/* -*- c++ -*- ----------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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|
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Copyright (2003) Sandia Corporation. Under the terms of Contract
|
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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.
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------------------------------------------------------------------------- */
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#ifdef KSPACE_CLASS
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KSpaceStyle(pppm,PPPM)
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#else
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#ifndef LMP_PPPM_H
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#define LMP_PPPM_H
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#include "lmptype.h"
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#include "mpi.h"
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#ifdef FFT_SINGLE
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typedef float FFT_SCALAR;
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#define MPI_FFT_SCALAR MPI_FLOAT
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#else
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typedef double FFT_SCALAR;
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#define MPI_FFT_SCALAR MPI_DOUBLE
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#endif
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#include "kspace.h"
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namespace LAMMPS_NS {
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class PPPM : public KSpace {
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public:
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PPPM(class LAMMPS *, int, char **);
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virtual ~PPPM();
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virtual void init();
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virtual void setup();
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void setup_grid();
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virtual void compute(int, int);
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virtual int timing_1d(int, double &);
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virtual int timing_3d(int, double &);
|
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virtual double memory_usage();
|
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|
||||
virtual void compute_group_group(int, int, int);
|
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|
||||
protected:
|
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int me,nprocs;
|
||||
int nfactors;
|
||||
int *factors;
|
||||
double qsum,qsqsum,q2;
|
||||
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 CommGrid *cg;
|
||||
class CommGrid *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
|
||||
|
||||
void set_grid_global();
|
||||
void set_grid_local();
|
||||
void adjust_gewald();
|
||||
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();
|
||||
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);
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
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: 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: Kspace style requires atom attribute q
|
||||
|
||||
The atom style defined does not have these attributes.
|
||||
|
||||
E: Cannot use nonperiodic 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 a long-range
|
||||
Coulombic or dispersion component be used.
|
||||
|
||||
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.
|
||||
|
||||
E: Cannot (yet) use PPPM with triclinic box and TIP4P
|
||||
|
||||
This feature is not yet supported.
|
||||
|
||||
E: Cannot use kspace solver on system with no charge
|
||||
|
||||
No atoms in system have a non-zero charge.
|
||||
|
||||
W: System is not charge neutral, net charge = %g
|
||||
|
||||
The total charge on all atoms on the system is not 0.0, which
|
||||
is not valid for the long-range Coulombic solvers.
|
||||
|
||||
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: 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: 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
|
||||
|
||||
This option is not yet supported.
|
||||
|
||||
E: Cannot (yet) use 'kspace_modify diff ad' with compute group/group
|
||||
|
||||
This option is not yet supported.
|
||||
|
||||
*/
|
||||
|
|
|
|||
Loading…
Reference in New Issue