diff --git a/Makefile b/Makefile index 5370032..90e3ce1 100644 --- a/Makefile +++ b/Makefile @@ -1,5 +1,3 @@ -TAG = CLANG - #CONFIGURE BUILD SYSTEM TARGET = MDBench-$(TAG) BUILD_DIR = ./$(TAG) @@ -8,14 +6,23 @@ MAKE_DIR = ./ Q ?= @ #DO NOT EDIT BELOW +include $(MAKE_DIR)/config.mk include $(MAKE_DIR)/include_$(TAG).mk INCLUDES += -I./src/includes +ifeq ($(strip $(DATA_LAYOUT)),AOS) +DEFINES += -DAOS +endif +ifeq ($(strip $(DATA_TYPE)),SP) +DEFINES += -DPRECISION=1 +else +DEFINES += -DPRECISION=2 +endif + VPATH = $(SRC_DIR) ASM = $(patsubst $(SRC_DIR)/%.c, $(BUILD_DIR)/%.s,$(wildcard $(SRC_DIR)/*.c)) OBJ = $(patsubst $(SRC_DIR)/%.c, $(BUILD_DIR)/%.o,$(wildcard $(SRC_DIR)/*.c)) -CPPFLAGS := $(CPPFLAGS) $(DEFINES) $(INCLUDES) - +CPPFLAGS := $(CPPFLAGS) $(DEFINES) $(OPTIONS) $(INCLUDES) ${TARGET}: $(BUILD_DIR) $(OBJ) @echo "===> LINKING $(TARGET)" diff --git a/README.md b/README.md index ba47bcb..94e2875 100644 --- a/README.md +++ b/README.md @@ -4,9 +4,10 @@ A simple, sequential C implementation of the [Mantevo miniMD](https://github.co ## Build -1. Open the `Makefile` and edit the `TAG` value according to the tool chain used. Currently supported is GCC, CLANG (LLVM), and ICC (Intel). -2. Open and adapt the compiler flags in `.mk`, e.g. in `include_ICC.mk` for the Intel tool chain. -3. Build the binary calling `make`. +1. Open `config.mk` and edit the `TAG` value according to the tool chain used. Currently supported is GCC, CLANG (LLVM), and ICC (Intel). +2. Change `DATA_LAYOUT` and `DATA_TYPE` if desired in config.mk. +3. Open and adapt the compiler flags in `.mk`, e.g. in `include_ICC.mk` for the Intel tool chain. +4. Build the binary calling `make`. You can clean intermediate build results with `make clean`, and all build results with `make distclean`. You have to call `make clean` before `make` if you changed the build settings. diff --git a/config.mk b/config.mk new file mode 100644 index 0000000..9cf51d0 --- /dev/null +++ b/config.mk @@ -0,0 +1,7 @@ +# Supported: GCC, CLANG, ICC +TAG ?= GCC +DATA_TYPE ?= SP#SP or DP +DATA_LAYOUT ?= SoA#AOS or SOA + +#Feature options +OPTIONS += -DALIGNMENT=64 diff --git a/include_CLANG.mk b/include_CLANG.mk index 68e0076..59fa579 100644 --- a/include_CLANG.mk +++ b/include_CLANG.mk @@ -1,5 +1,4 @@ CC = cc -CXX = cc LINKER = $(CC) ANSI_CFLAGS = -ansi @@ -7,11 +6,9 @@ ANSI_CFLAGS += -std=c99 ANSI_CFLAGS += -pedantic ANSI_CFLAGS += -Wextra -CFLAGS = -Ofast $(ANSI_CFLAGS) -Xpreprocessor -fopenmp #-g +CFLAGS = -Ofast $(ANSI_CFLAGS) -g #-Xpreprocessor -fopenmp -g ASFLAGS = -masm=intel -CXXFLAGS = $(CFLAGS) -FCFLAGS = LFLAGS = -DEFINES = -D_GNU_SOURCE -DALIGNMENT=64 -DPRECISION=2 +DEFINES = -D_GNU_SOURCE INCLUDES = -LIBS = -lomp +LIBS = -lm #-lomp diff --git a/include_GCC.mk b/include_GCC.mk index 83b5c5b..d29cca9 100644 --- a/include_GCC.mk +++ b/include_GCC.mk @@ -1,7 +1,5 @@ CC = gcc -CXX = g++ -FC = gfortran -LINKER = $(CXX) +LINKER = $(CC) ANSI_CFLAGS = -ansi ANSI_CFLAGS += -std=c99 @@ -9,13 +7,9 @@ ANSI_CFLAGS += -pedantic ANSI_CFLAGS += -Wextra # CFLAGS = -O0 -g -std=c99 -fargument-noalias -CFLAGS = -O3 -march=znver1 -ffast-math -funroll-loops -fopenmp -CXXFLAGS = $(CFLAGS) +CFLAGS = -O3 -march=znver1 -ffast-math -funroll-loops # -fopenmp ASFLAGS = -masm=intel -FCFLAGS = LFLAGS = DEFINES = -D_GNU_SOURCE INCLUDES = -LIBS = - - +LIBS = -lm diff --git a/include_ICC.mk b/include_ICC.mk index 25207af..ddb61ac 100644 --- a/include_ICC.mk +++ b/include_ICC.mk @@ -1,5 +1,4 @@ CC = icc -CXX = icpc LINKER = $(CC) OPENMP = #-qopenmp @@ -11,10 +10,8 @@ PROFILE = #-profile-functions -g -pg #OPTS = -fast -no-vec $(PROFILE) OPTS = -fast -xHost $(PROFILE) CFLAGS = $(PROFILE) -restrict $(OPENMP) $(OPTS) -CXXFLAGS = $(CFLAGS) ASFLAGS = -masm=intel -FCFLAGS = LFLAGS = $(PROFILE) $(OPTS) $(OPENMP) -DEFINES = -D_GNU_SOURCE -DALIGNMENT=64 # -DLIKWID_PERFMON -DPRECISION=1 +DEFINES = -D_GNU_SOURCE # -DALIGNMENT=64 -DLIKWID_PERFMON -DPRECISION=1 INCLUDES = #$(LIKWID_INC) -LIBS = #$(LIKWID_LIB) -llikwid +LIBS = -lm #$(LIKWID_LIB) -llikwid diff --git a/src/atom.c b/src/atom.c index 313ffdc..687de55 100644 --- a/src/atom.c +++ b/src/atom.c @@ -1,8 +1,10 @@ /* * ======================================================================================= * - * Author: Jan Eitzinger (je), jan.eitzinger@fau.de - * Copyright (c) 2020 RRZE, University Erlangen-Nuremberg + * Authors: Jan Eitzinger (je), jan.eitzinger@fau.de + * Rafael Ravedutti (rr), rafaelravedutti@gmail.com + * + * Copyright (c) 2021 RRZE, University Erlangen-Nuremberg * * This file is part of MD-Bench. * @@ -111,9 +113,9 @@ void createAtom(Atom *atom, Parameter *param) growAtom(atom); } - atom->x[atom->Nlocal] = xtmp; - atom->y[atom->Nlocal] = ytmp; - atom->z[atom->Nlocal] = ztmp; + atom_x(atom->Nlocal) = xtmp; + atom_y(atom->Nlocal) = ytmp; + atom_z(atom->Nlocal) = ztmp; atom->vx[atom->Nlocal] = vxtmp; atom->vy[atom->Nlocal] = vytmp; atom->vz[atom->Nlocal] = vztmp; @@ -136,9 +138,13 @@ void growAtom(Atom *atom) int nold = atom->Nmax; atom->Nmax += DELTA; + #ifdef AOS + atom->x = (MD_FLOAT*) reallocate(atom->x, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT) * 3, nold * sizeof(MD_FLOAT) * 3); + #else atom->x = (MD_FLOAT*) reallocate(atom->x, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT)); atom->y = (MD_FLOAT*) reallocate(atom->y, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT)); atom->z = (MD_FLOAT*) reallocate(atom->z, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT)); + #endif atom->vx = (MD_FLOAT*) reallocate(atom->vx, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT)); atom->vy = (MD_FLOAT*) reallocate(atom->vy, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT)); atom->vz = (MD_FLOAT*) reallocate(atom->vz, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT)); diff --git a/src/includes/atom.h b/src/includes/atom.h index 97e0429..e090936 100644 --- a/src/includes/atom.h +++ b/src/includes/atom.h @@ -2,7 +2,7 @@ * ======================================================================================= * * Author: Jan Eitzinger (je), jan.eitzinger@fau.de - * Copyright (c) 2020 RRZE, University Erlangen-Nuremberg + * Copyright (c) 2021 RRZE, University Erlangen-Nuremberg * * This file is part of MD-Bench. * @@ -35,4 +35,17 @@ typedef struct { extern void initAtom(Atom*); extern void createAtom(Atom*, Parameter*); extern void growAtom(Atom*); + +#ifdef AOS +#define POS_DATA_LAYOUT "AoS" +#define atom_x(i) atom->x[(i) * 3 + 0] +#define atom_y(i) atom->x[(i) * 3 + 1] +#define atom_z(i) atom->x[(i) * 3 + 2] +#else +#define POS_DATA_LAYOUT "SoA" +#define atom_x(i) atom->x[i] +#define atom_y(i) atom->y[i] +#define atom_z(i) atom->z[i] +#endif + #endif diff --git a/src/includes/parameter.h b/src/includes/parameter.h index 87da5f8..4f6f914 100644 --- a/src/includes/parameter.h +++ b/src/includes/parameter.h @@ -23,9 +23,6 @@ #ifndef __PARAMETER_H_ #define __PARAMETER_H_ -#ifndef PRECISION -#define PRECISION 2 -#endif #if PRECISION == 1 #define MD_FLOAT float #else diff --git a/src/main.c b/src/main.c index 7fb68d1..c064815 100644 --- a/src/main.c +++ b/src/main.c @@ -116,7 +116,6 @@ double reneighbour( void initialIntegrate(Parameter *param, Atom *atom) { - MD_FLOAT* x = atom->x; MD_FLOAT* y = atom->y; MD_FLOAT* z = atom->z; MD_FLOAT* fx = atom->fx; MD_FLOAT* fy = atom->fy; MD_FLOAT* fz = atom->fz; MD_FLOAT* vx = atom->vx; MD_FLOAT* vy = atom->vy; MD_FLOAT* vz = atom->vz; @@ -124,9 +123,9 @@ void initialIntegrate(Parameter *param, Atom *atom) vx[i] += param->dtforce * fx[i]; vy[i] += param->dtforce * fy[i]; vz[i] += param->dtforce * fz[i]; - x[i] += param->dt * vx[i]; - y[i] += param->dt * vy[i]; - z[i] += param->dt * vz[i]; + atom_x(i) = atom_x(i) + param->dt * vx[i]; + atom_y(i) = atom_y(i) + param->dt * vy[i]; + atom_z(i) = atom_z(i) + param->dt * vz[i]; } } @@ -149,7 +148,6 @@ double computeForce(Parameter *param, Atom *atom, Neighbor *neighbor) MD_FLOAT cutforcesq = param->cutforce * param->cutforce; MD_FLOAT sigma6 = param->sigma6; MD_FLOAT epsilon = param->epsilon; - MD_FLOAT* x = atom->x; MD_FLOAT* y = atom->y; MD_FLOAT* z = atom->z; MD_FLOAT* fx = atom->fx; MD_FLOAT* fy = atom->fy; MD_FLOAT* fz = atom->fz; MD_FLOAT S, E; @@ -166,9 +164,9 @@ double computeForce(Parameter *param, Atom *atom, Neighbor *neighbor) for(int i = 0; i < Nlocal; i++) { neighs = &neighbor->neighbors[i * neighbor->maxneighs]; int numneighs = neighbor->numneigh[i]; - MD_FLOAT xtmp = x[i]; - MD_FLOAT ytmp = y[i]; - MD_FLOAT ztmp = z[i]; + MD_FLOAT xtmp = atom_x(i); + MD_FLOAT ytmp = atom_y(i); + MD_FLOAT ztmp = atom_z(i); MD_FLOAT fix = 0; MD_FLOAT fiy = 0; @@ -176,9 +174,9 @@ double computeForce(Parameter *param, Atom *atom, Neighbor *neighbor) for(int k = 0; k < numneighs; k++) { int j = neighs[k]; - MD_FLOAT delx = xtmp - x[j]; - MD_FLOAT dely = ytmp - y[j]; - MD_FLOAT delz = ztmp - z[j]; + MD_FLOAT delx = xtmp - atom_x(j); + MD_FLOAT dely = ytmp - atom_y(j); + MD_FLOAT delz = ztmp - atom_z(j); MD_FLOAT rsq = delx * delx + dely * dely + delz * delz; if(rsq < cutforcesq) { @@ -293,6 +291,7 @@ int main (int argc, char** argv) computeThermo(-1, ¶m, &atom); printf(HLINE); + printf("Data layout for positions: %s\n", POS_DATA_LAYOUT); #if PRECISION == 1 printf("Using single precision floating point.\n"); #else diff --git a/src/neighbor.c b/src/neighbor.c index 7460efb..05591ed 100644 --- a/src/neighbor.c +++ b/src/neighbor.c @@ -2,7 +2,7 @@ * ======================================================================================= * * Author: Jan Eitzinger (je), jan.eitzinger@fau.de - * Copyright (c) 2020 RRZE, University Erlangen-Nuremberg + * Copyright (c) 2021 RRZE, University Erlangen-Nuremberg * * This file is part of MD-Bench. * @@ -184,9 +184,6 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor) /* bin local & ghost atoms */ binatoms(atom); int resize = 1; - MD_FLOAT* x = atom->x; - MD_FLOAT* y = atom->y; - MD_FLOAT* z = atom->z; /* loop over each atom, storing neighbors */ while(resize) { @@ -196,9 +193,9 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor) for(int i = 0; i < atom->Nlocal; i++) { int* neighptr = &(neighbor->neighbors[i * neighbor->maxneighs]); int n = 0; - MD_FLOAT xtmp = x[i]; - MD_FLOAT ytmp = y[i]; - MD_FLOAT ztmp = z[i]; + MD_FLOAT xtmp = atom_x(i); + MD_FLOAT ytmp = atom_y(i); + MD_FLOAT ztmp = atom_z(i); int ibin = coord2bin(xtmp, ytmp, ztmp); for(int k = 0; k < nstencil; k++) { @@ -212,9 +209,9 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor) continue; } - MD_FLOAT delx = xtmp - x[j]; - MD_FLOAT dely = ytmp - y[j]; - MD_FLOAT delz = ztmp - z[j]; + MD_FLOAT delx = xtmp - atom_x(j); + MD_FLOAT dely = ytmp - atom_y(j); + MD_FLOAT delz = ztmp - atom_z(j); MD_FLOAT rsq = delx * delx + dely * dely + delz * delz; if( rsq <= cutneighsq ) { @@ -309,9 +306,6 @@ int coord2bin(MD_FLOAT xin, MD_FLOAT yin, MD_FLOAT zin) void binatoms(Atom *atom) { int nall = atom->Nlocal + atom->Nghost; - MD_FLOAT* x = atom->x; - MD_FLOAT* y = atom->y; - MD_FLOAT* z = atom->z; int resize = 1; while(resize > 0) { @@ -322,7 +316,7 @@ void binatoms(Atom *atom) } for(int i = 0; i < nall; i++) { - int ibin = coord2bin(x[i], y[i], z[i]); + int ibin = coord2bin(atom_x(i), atom_y(i), atom_z(i)); if(bincount[ibin] < atoms_per_bin) { int ac = bincount[ibin]++; diff --git a/src/pbc.c b/src/pbc.c index 54ef7f8..6428669 100644 --- a/src/pbc.c +++ b/src/pbc.c @@ -48,17 +48,14 @@ void initPbc() void updatePbc(Atom *atom, Parameter *param) { int nlocal = atom->Nlocal; - MD_FLOAT* x = atom->x; - MD_FLOAT* y = atom->y; - MD_FLOAT* z = atom->z; MD_FLOAT xprd = param->xprd; MD_FLOAT yprd = param->yprd; MD_FLOAT zprd = param->zprd; for(int i = 0; i < atom->Nghost; i++) { - x[nlocal + i] = x[BorderMap[i]] + PBCx[i] * xprd; - y[nlocal + i] = y[BorderMap[i]] + PBCy[i] * yprd; - z[nlocal + i] = z[BorderMap[i]] + PBCz[i] * zprd; + atom_x(nlocal + i) = atom_x(BorderMap[i]) + PBCx[i] * xprd; + atom_y(nlocal + i) = atom_y(BorderMap[i]) + PBCy[i] * yprd; + atom_z(nlocal + i) = atom_z(BorderMap[i]) + PBCz[i] * zprd; } } @@ -66,31 +63,28 @@ void updatePbc(Atom *atom, Parameter *param) * to periodic boundary conditions */ void updateAtomsPbc(Atom *atom, Parameter *param) { - MD_FLOAT* x = atom->x; - MD_FLOAT* y = atom->y; - MD_FLOAT* z = atom->z; MD_FLOAT xprd = param->xprd; MD_FLOAT yprd = param->yprd; MD_FLOAT zprd = param->zprd; for(int i = 0; i < atom->Nlocal; i++) { - if(x[i] < 0.0) { - x[i] += xprd; - } else if(x[i] >= xprd) { - x[i] -= xprd; + if(atom_x(i) < 0.0) { + atom_x(i) += xprd; + } else if(atom_x(i) >= xprd) { + atom_x(i) -= xprd; } - if(y[i] < 0.0) { - y[i] += yprd; - } else if(y[i] >= yprd) { - y[i] -= yprd; + if(atom_y(i) < 0.0) { + atom_y(i) += yprd; + } else if(atom_y(i) >= yprd) { + atom_y(i) -= yprd; } - if(z[i] < 0.0) { - z[i] += zprd; - } else if(z[i] >= zprd) { - z[i] -= zprd; + if(atom_z(i) < 0.0) { + atom_z(i) += zprd; + } else if(atom_z(i) >= zprd) { + atom_z(i) -= zprd; } } } @@ -99,10 +93,14 @@ void updateAtomsPbc(Atom *atom, Parameter *param) * defining ghost atoms around domain * only creates mapping and coordinate corrections * that are then enforced in updatePbc */ -#define ADDGHOST(dx,dy,dz) Nghost++; BorderMap[Nghost] = i; PBCx[Nghost] = dx; PBCy[Nghost] = dy; PBCz[Nghost] = dz; +#define ADDGHOST(dx,dy,dz) \ + Nghost++; \ + BorderMap[Nghost] = i; \ + PBCx[Nghost] = dx; \ + PBCy[Nghost] = dy; \ + PBCz[Nghost] = dz; void setupPbc(Atom *atom, Parameter *param) { - MD_FLOAT* x = atom->x; MD_FLOAT* y = atom->y; MD_FLOAT* z = atom->z; MD_FLOAT xprd = param->xprd; MD_FLOAT yprd = param->yprd; MD_FLOAT zprd = param->zprd; @@ -113,42 +111,45 @@ void setupPbc(Atom *atom, Parameter *param) if (atom->Nlocal + Nghost + 7 >= atom->Nmax) { growAtom(atom); - x = atom->x; y = atom->y; z = atom->z; } if (Nghost + 7 >= NmaxGhost) { growPbc(); } + MD_FLOAT x = atom_x(i); + MD_FLOAT y = atom_y(i); + MD_FLOAT z = atom_z(i); + /* Setup ghost atoms */ /* 6 planes */ - if (x[i] < Cutneigh) { ADDGHOST(+1,0,0); } - if (x[i] >= (xprd-Cutneigh)) { ADDGHOST(-1,0,0); } - if (y[i] < Cutneigh) { ADDGHOST(0,+1,0); } - if (y[i] >= (yprd-Cutneigh)) { ADDGHOST(0,-1,0); } - if (z[i] < Cutneigh) { ADDGHOST(0,0,+1); } - if (z[i] >= (zprd-Cutneigh)) { ADDGHOST(0,0,-1); } + if (x < Cutneigh) { ADDGHOST(+1,0,0); } + if (x >= (xprd-Cutneigh)) { ADDGHOST(-1,0,0); } + if (y < Cutneigh) { ADDGHOST(0,+1,0); } + if (y >= (yprd-Cutneigh)) { ADDGHOST(0,-1,0); } + if (z < Cutneigh) { ADDGHOST(0,0,+1); } + if (z >= (zprd-Cutneigh)) { ADDGHOST(0,0,-1); } /* 8 corners */ - if (x[i] < Cutneigh && y[i] < Cutneigh && z[i] < Cutneigh) { ADDGHOST(+1,+1,+1); } - if (x[i] < Cutneigh && y[i] >= (yprd-Cutneigh) && z[i] < Cutneigh) { ADDGHOST(+1,-1,+1); } - if (x[i] < Cutneigh && y[i] >= Cutneigh && z[i] >= (zprd-Cutneigh)) { ADDGHOST(+1,+1,-1); } - if (x[i] < Cutneigh && y[i] >= (yprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { ADDGHOST(+1,-1,-1); } - if (x[i] >= (xprd-Cutneigh) && y[i] < Cutneigh && z[i] < Cutneigh) { ADDGHOST(-1,+1,+1); } - if (x[i] >= (xprd-Cutneigh) && y[i] >= (yprd-Cutneigh) && z[i] < Cutneigh) { ADDGHOST(-1,-1,+1); } - if (x[i] >= (xprd-Cutneigh) && y[i] < Cutneigh && z[i] >= (zprd-Cutneigh)) { ADDGHOST(-1,+1,-1); } - if (x[i] >= (xprd-Cutneigh) && y[i] >= (yprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { ADDGHOST(-1,-1,-1); } + if (x < Cutneigh && y < Cutneigh && z < Cutneigh) { ADDGHOST(+1,+1,+1); } + if (x < Cutneigh && y >= (yprd-Cutneigh) && z < Cutneigh) { ADDGHOST(+1,-1,+1); } + if (x < Cutneigh && y >= Cutneigh && z >= (zprd-Cutneigh)) { ADDGHOST(+1,+1,-1); } + if (x < Cutneigh && y >= (yprd-Cutneigh) && z >= (zprd-Cutneigh)) { ADDGHOST(+1,-1,-1); } + if (x >= (xprd-Cutneigh) && y < Cutneigh && z < Cutneigh) { ADDGHOST(-1,+1,+1); } + if (x >= (xprd-Cutneigh) && y >= (yprd-Cutneigh) && z < Cutneigh) { ADDGHOST(-1,-1,+1); } + if (x >= (xprd-Cutneigh) && y < Cutneigh && z >= (zprd-Cutneigh)) { ADDGHOST(-1,+1,-1); } + if (x >= (xprd-Cutneigh) && y >= (yprd-Cutneigh) && z >= (zprd-Cutneigh)) { ADDGHOST(-1,-1,-1); } /* 12 edges */ - if (x[i] < Cutneigh && z[i] < Cutneigh) { ADDGHOST(+1,0,+1); } - if (x[i] < Cutneigh && z[i] >= (zprd-Cutneigh)) { ADDGHOST(+1,0,-1); } - if (x[i] >= (xprd-Cutneigh) && z[i] < Cutneigh) { ADDGHOST(-1,0,+1); } - if (x[i] >= (xprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { ADDGHOST(-1,0,-1); } - if (y[i] < Cutneigh && z[i] < Cutneigh) { ADDGHOST(0,+1,+1); } - if (y[i] < Cutneigh && z[i] >= (zprd-Cutneigh)) { ADDGHOST(0,+1,-1); } - if (y[i] >= (yprd-Cutneigh) && z[i] < Cutneigh) { ADDGHOST(0,-1,+1); } - if (y[i] >= (yprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { ADDGHOST(0,-1,-1); } - if (y[i] < Cutneigh && x[i] < Cutneigh) { ADDGHOST(+1,+1,0); } - if (y[i] < Cutneigh && x[i] >= (xprd-Cutneigh)) { ADDGHOST(-1,+1,0); } - if (y[i] >= (yprd-Cutneigh) && x[i] < Cutneigh) { ADDGHOST(+1,-1,0); } - if (y[i] >= (yprd-Cutneigh) && x[i] >= (xprd-Cutneigh)) { ADDGHOST(-1,-1,0); } + if (x < Cutneigh && z < Cutneigh) { ADDGHOST(+1,0,+1); } + if (x < Cutneigh && z >= (zprd-Cutneigh)) { ADDGHOST(+1,0,-1); } + if (x >= (xprd-Cutneigh) && z < Cutneigh) { ADDGHOST(-1,0,+1); } + if (x >= (xprd-Cutneigh) && z >= (zprd-Cutneigh)) { ADDGHOST(-1,0,-1); } + if (y < Cutneigh && z < Cutneigh) { ADDGHOST(0,+1,+1); } + if (y < Cutneigh && z >= (zprd-Cutneigh)) { ADDGHOST(0,+1,-1); } + if (y >= (yprd-Cutneigh) && z < Cutneigh) { ADDGHOST(0,-1,+1); } + if (y >= (yprd-Cutneigh) && z >= (zprd-Cutneigh)) { ADDGHOST(0,-1,-1); } + if (y < Cutneigh && x < Cutneigh) { ADDGHOST(+1,+1,0); } + if (y < Cutneigh && x >= (xprd-Cutneigh)) { ADDGHOST(-1,+1,0); } + if (y >= (yprd-Cutneigh) && x < Cutneigh) { ADDGHOST(+1,-1,0); } + if (y >= (yprd-Cutneigh) && x >= (xprd-Cutneigh)) { ADDGHOST(-1,-1,0); } } // increase by one to make it the ghost atom count atom->Nghost = Nghost + 1;