support for tiled decompositions in PPPM
This commit is contained in:
Steve Plimpton
1093
src/KSPACE/gridcomm2.cpp
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1093
src/KSPACE/gridcomm2.cpp
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File diff suppressed because it is too large
Load Diff
201
src/KSPACE/gridcomm2.h
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201
src/KSPACE/gridcomm2.h
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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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#ifndef LMP_GRIDCOMM2_H
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#define LMP_GRIDCOMM2_H
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#include "pointers.h"
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namespace LAMMPS_NS {
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class GridComm2 : protected Pointers {
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public:
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GridComm2(class LAMMPS *, MPI_Comm, int, int, int,
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int, int, int, int, int, int,
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int, int, int, int, int, int);
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GridComm2(class LAMMPS *, MPI_Comm, int, int, int,
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int, int, int, int, int, int,
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int, int, int, int, int, int,
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int, int, int, int, int, int);
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~GridComm2();
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void setup(int &, int &);
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int ghost_adjacent();
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void forward_comm(class KSpace *, int, int, int, void *, void *, MPI_Datatype);
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void reverse_comm(class KSpace *, int, int, int, void *, void *, MPI_Datatype);
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private:
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int me,nprocs;
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int layout; // REGULAR or TILED
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MPI_Comm gridcomm;
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// inputs from caller via constructor
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int nx,ny,nz; // size of global grid in all 3 dims
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int inxlo,inxhi; // inclusive extent of my grid chunk
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int inylo,inyhi; // 0 <= in <= N-1
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int inzlo,inzhi;
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int outxlo,outxhi; // inclusive extent of my grid chunk plus
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int outylo,outyhi; // ghost cells in all 6 directions
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int outzlo,outzhi; // lo indices can be < 0, hi indices can be >= N
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int outxlo_max,outxhi_max; // ??
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int outylo_max,outyhi_max;
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int outzlo_max,outzhi_max;
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// -------------------------------------------
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// internal variables for REGULAR layout
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// -------------------------------------------
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int procxlo,procxhi; // 6 neighbor procs that adjoin me
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int procylo,procyhi; // not used for comm_style = tiled
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int proczlo,proczhi;
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int ghostxlo,ghostxhi; // # of my owned grid planes needed
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int ghostylo,ghostyhi; // by neighobr procs in each dir as their ghost planes
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int ghostzlo,ghostzhi;
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// swap = exchange of owned and ghost grid cells between 2 procs, including self
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struct Swap {
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int sendproc; // proc to send to for forward comm
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int recvproc; // proc to recv from for forward comm
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int npack; // # of datums to pack
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int nunpack; // # of datums to unpack
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int *packlist; // 3d array offsets to pack
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int *unpacklist; // 3d array offsets to unpack
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};
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int nswap,maxswap;
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Swap *swap;
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// -------------------------------------------
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// internal variables for TILED layout
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// -------------------------------------------
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int *overlap_procs;
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MPI_Request *requests;
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// RCB tree of cut info
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// each proc contributes one value, except proc 0
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struct RCBinfo {
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int dim; // 0,1,2 = which dim the cut is in
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int cut; // grid index of lowest cell in upper half of cut
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};
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RCBinfo *rcbinfo;
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// overlap = a proc whose owned cells overlap with my extended ghost box
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// includes overlaps across periodic boundaries, can also be self
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struct Overlap {
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int proc; // proc whose owned cells overlap my ghost cells
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int box[6]; // box that overlaps otherproc's owned cells
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// this box is wholly contained within global grid
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int pbc[3]; // PBC offsets to convert box to a portion of my ghost box
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// my ghost box may extend beyond global grid
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};
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int noverlap,maxoverlap;
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Overlap *overlap;
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// request = sent to each proc whose owned cells overlap my ghost cells
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struct Request {
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int sender; // sending proc
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int index; // index of overlap on sender
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int box[6]; // box that overlaps receiver's owned cells
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// wholly contained within global grid
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};
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Request *srequest,*rrequest;
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// response = reply from each proc whose owned cells overlap my ghost cells
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struct Response {
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int index; // index of my overlap for the initial request
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int box[6]; // box that overlaps responder's owned cells
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// wholly contained within global grid
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// has to unwrapped by PBC to map to my ghost cells
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};
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Response *sresponse,*rresponse;
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// send = proc to send a subset of my owned cells to, for forward comm
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// for reverse comm, proc I receive ghost overlaps with my owned cells from
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// offset used in reverse comm to recv a message in middle of a large buffer
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struct Send {
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int proc;
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int npack;
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int *packlist;
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int offset;
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};
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// recv = proc to recv a subset of my ghost cells from, for forward comm
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// for reverse comm, proc I send a subset of my ghost cells to
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// offset used in forward comm to recv a message in middle of a large buffer
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struct Recv {
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int proc;
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int nunpack;
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int *unpacklist;
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int offset;
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};
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int adjacent; // 0 on a proc who receives ghosts from a non-neighbor proc
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// copy = subset of my owned cells to copy into subset of my ghost cells
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// that describes forward comm, for reverse comm it is the opposite
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struct Copy {
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int npack;
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int nunpack;
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int *packlist;
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int *unpacklist;
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};
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int nsend,nrecv,ncopy;
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Send *send;
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Recv *recv;
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Copy *copy;
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// -------------------------------------------
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// internal methods
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// -------------------------------------------
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void setup_regular(int &, int &);
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void setup_tiled(int &, int &);
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void ghost_box_drop(int *, int *);
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void box_drop_grid(int *, int, int, int &, int *);
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int ghost_adjacent_regular();
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int ghost_adjacent_tiled();
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void forward_comm_regular(class KSpace *, int, int, int,
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void *, void *, MPI_Datatype);
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void forward_comm_tiled(class KSpace *, int, int, int,
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void *, void *, MPI_Datatype);
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void reverse_comm_regular(class KSpace *, int, int, int,
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void *, void *, MPI_Datatype);
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void reverse_comm_tiled(class KSpace *, int, int, int,
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void *, void *, MPI_Datatype);
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void grow_swap();
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void grow_overlap();
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int indices(int *&, int, int, int, int, int, int);
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};
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}
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#endif
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3524
src/KSPACE/pppm2.cpp
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3524
src/KSPACE/pppm2.cpp
Normal file
File diff suppressed because it is too large
Load Diff
360
src/KSPACE/pppm2.h
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360
src/KSPACE/pppm2.h
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@ -0,0 +1,360 @@
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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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|
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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(pppm2,PPPM2)
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#else
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#ifndef LMP_PPPM2_H
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#define LMP_PPPM2_H
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#include "kspace.h"
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#if defined(FFT_FFTW3)
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#define LMP_FFT_LIB "FFTW3"
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#elif defined(FFT_MKL)
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#define LMP_FFT_LIB "MKL FFT"
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#elif defined(FFT_CUFFT)
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#define LMP_FFT_LIB "cuFFT"
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#else
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#define LMP_FFT_LIB "KISS FFT"
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#endif
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#ifdef FFT_SINGLE
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typedef float FFT_SCALAR;
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#define LMP_FFT_PREC "single"
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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 LMP_FFT_PREC "double"
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#define MPI_FFT_SCALAR MPI_DOUBLE
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#endif
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namespace LAMMPS_NS {
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class PPPM2 : public KSpace {
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public:
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PPPM2(class LAMMPS *);
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virtual ~PPPM2();
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virtual void settings(int, char **);
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virtual void init();
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virtual void setup();
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virtual 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 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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|
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// FFTs and grid communication
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|
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class FFT3d *fft1,*fft2;
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class Remap *remap;
|
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class GridComm2 *gc;
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FFT_SCALAR *gc_buf1,*gc_buf2;
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int ngc_buf1,ngc_buf2,npergrid;
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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;
|
||||||
|
FFT_SCALAR *density_A_fft,*density_B_fft;
|
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|
||||||
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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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|
||||||
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virtual void set_grid_global();
|
||||||
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void set_grid_local();
|
||||||
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void adjust_gewald();
|
||||||
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virtual 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();
|
||||||
|
virtual void deallocate_peratom();
|
||||||
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int factorable(int);
|
||||||
|
double compute_df_kspace();
|
||||||
|
double estimate_ik_error(double, double, bigint);
|
||||||
|
virtual double compute_qopt();
|
||||||
|
virtual void compute_gf_denom();
|
||||||
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virtual void compute_gf_ik();
|
||||||
|
virtual void compute_gf_ad();
|
||||||
|
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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||||||
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virtual void poisson();
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||||||
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virtual void poisson_ik();
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||||||
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virtual void poisson_ad();
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||||||
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|
||||||
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virtual void fieldforce();
|
||||||
|
virtual void fieldforce_ik();
|
||||||
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virtual void fieldforce_ad();
|
||||||
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|
||||||
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virtual void poisson_peratom();
|
||||||
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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();
|
||||||
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|
||||||
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// grid communication
|
||||||
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|
||||||
|
virtual void pack_forward2(int, void *, int, int *);
|
||||||
|
virtual void unpack_forward2(int, void *, int, int *);
|
||||||
|
virtual void pack_reverse2(int, void *, int, int *);
|
||||||
|
virtual void unpack_reverse2(int, void *, int, int *);
|
||||||
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|
||||||
|
// 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.
|
||||||
|
|
||||||
|
*/
|
||||||
@ -665,9 +665,9 @@ void Force::create_kspace(const std::string &style, int trysuffix)
|
|||||||
kspace = new_kspace(style,trysuffix,sflag);
|
kspace = new_kspace(style,trysuffix,sflag);
|
||||||
store_style(kspace_style,style,sflag);
|
store_style(kspace_style,style,sflag);
|
||||||
|
|
||||||
if (comm->style == 1 && !kspace_match("ewald",0))
|
//if (comm->style == 1 && !kspace_match("ewald",0))
|
||||||
error->all(FLERR,
|
// error->all(FLERR,
|
||||||
"Cannot yet use KSpace solver with grid with comm style tiled");
|
// "Cannot yet use KSpace solver with grid with comm style tiled");
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
|
|||||||
@ -126,6 +126,11 @@ class KSpace : protected Pointers {
|
|||||||
virtual void pack_reverse(int, FFT_SCALAR *, int, int *) {};
|
virtual void pack_reverse(int, FFT_SCALAR *, int, int *) {};
|
||||||
virtual void unpack_reverse(int, FFT_SCALAR *, int, int *) {};
|
virtual void unpack_reverse(int, FFT_SCALAR *, int, int *) {};
|
||||||
|
|
||||||
|
virtual void pack_forward2(int, void *, int, int *) {};
|
||||||
|
virtual void unpack_forward2(int, void *, int, int *) {};
|
||||||
|
virtual void pack_reverse2(int, void *, int, int *) {};
|
||||||
|
virtual void unpack_reverse2(int, void *, int, int *) {};
|
||||||
|
|
||||||
virtual int timing(int, double &, double &) {return 0;}
|
virtual int timing(int, double &, double &) {return 0;}
|
||||||
virtual int timing_1d(int, double &) {return 0;}
|
virtual int timing_1d(int, double &) {return 0;}
|
||||||
virtual int timing_3d(int, double &) {return 0;}
|
virtual int timing_3d(int, double &) {return 0;}
|
||||||
|
|||||||
Reference in New Issue
Block a user