ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14805 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2016-04-07 21:04:44 +00:00
parent 65f40aa34d
commit 8e36364f5c
26 changed files with 314 additions and 145 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
src/ASPHERE/pair_line_lj.cpp
View File

@ -69,11 +69,11 @@ PairLineLJ::~PairLineLJ()
void PairLineLJ::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype,tmp;
int i,j,ii,jj,inum,jnum,itype,jtype;
int ni,nj,npi,npj,ifirst,jfirst;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r2inv,r6inv,term1,term2,sig,sig3,forcelj;
double xi[2],xj[2],fi[2],fj[2],dxi,dxj,dyi,dyj;
double xi[2],xj[2],fi[2],dxi,dxj,dyi,dyj;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;

85
src/DEPEND/fastdep.c
View File

@ -33,7 +33,24 @@
#include <sys/types.h>
#include <sys/stat.h>
const char version[] = "2.0";
const char version[] = "2.1";
/* store list of accepted extensions for object targets */
static const char *extensions[] = { ".cpp", ".c", ".cu" };
static const int numextensions = sizeof(extensions)/sizeof(const char *);
/* strdup() is not part of ANSI C. provide a replacement for portability */
static char *my_strdup(const char *src)
{
int len;
char *ptr;
if (src == NULL) return NULL;
len = strlen(src);
ptr = (char *)malloc(len+1);
if (ptr) memcpy(ptr,src,len+1);
return ptr;
}
/************************************************************************
* utility functions
@ -198,7 +215,7 @@ static void llist_append(llist_t *ll, const char *key)
llnode_t *tmp;
if ((ll == NULL) || (key == NULL)) return;
ll->tail->key = strdup(key);
ll->tail->key = my_strdup(key);
ll->count ++;
tmp = (llnode_t *)malloc(sizeof(llnode_t));
tmp->key = NULL;
@ -286,7 +303,7 @@ static void set_add(set_t *s, const char *key)
tmp = tmp->next;
}
s->count ++;
tmp->key = strdup(key);
tmp->key = my_strdup(key);
tmp->next = (llnode_t *)malloc(sizeof(llnode_t));
tmp = tmp->next;
tmp->key = NULL;
@ -375,7 +392,7 @@ static void map_add(map_t *m, const char *key, const char *val)
/* add new entry to map */
if (tmp->next == NULL) {
m->count ++;
tmp->key = strdup(key);
tmp->key = my_strdup(key);
tmp->val = set_init(50); /* XXX: chosen arbitrarily */
tmp->next = (mapnode_t *)malloc(sizeof(mapnode_t));
tmp->next->key = NULL;
@ -547,42 +564,52 @@ static void do_depend(llnode_t *head, map_t *deps)
set_t *incl;
const char *source;
char *target, *ptr;
int i,num;
int i,num,ext;
tmp = head;
while (tmp->next != NULL) {
source = tmp->key;
target = strrchr(source,'/');
if (target == NULL) {
target = strdup(source);
target = my_strdup(source);
} else {
target = strdup(target+1);
target = my_strdup(target+1);
}
ext = 0;
ptr = strrchr(target,'.');
if (ptr != NULL) {
ptr[1] = 'o';
ptr[2] = '\0';
}
fputs(target,stdout);
fputs(" : ",stdout);
fputs(source,stdout);
free((void *)target);
incl = set_init(50);
add_depend(source,incl,deps);
num = incl->nbuckets;
for (i = 0; i < num; ++i) {
lnk = incl->buckets + i;
while (lnk->next != NULL) {
fputc(' ',stdout);
fputs(lnk->key,stdout);
lnk = lnk->next;
for (i = 0; i < numextensions; ++i) {
if (strcmp(ptr,extensions[i]) == 0) ++ext;
}
if (ext > 0) {
ptr[1] = 'o';
ptr[2] = '\0';
}
}
fputc('\n',stdout);
set_free(incl);
if (ext > 0) {
fputs(target,stdout);
fputs(" : ",stdout);
fputs(source,stdout);
incl = set_init(50);
add_depend(source,incl,deps);
num = incl->nbuckets;
for (i = 0; i < num; ++i) {
lnk = incl->buckets + i;
while (lnk->next != NULL) {
fputc(' ',stdout);
fputs(lnk->key,stdout);
lnk = lnk->next;
}
}
fputc('\n',stdout);
set_free(incl);
}
free((void *)target);
tmp = tmp->next;
}
}
@ -601,6 +628,8 @@ int main(int argc, char **argv)
fprintf(stderr,"FastDep v%s for LAMMPS\n"
"Usage: %s [-I <path> ...] -- <src1> [<src2> ...]\n",
version,argv[0]);
fprintf(stderr,"Supported extensions: %d, %s, %s\n",numextensions,
extensions[0], extensions[1]);
return 1;
}
@ -631,7 +660,7 @@ int main(int argc, char **argv)
}
} else if (strcmp(*argv,"--") == 0) {
break;
} // ignore all unrecognized arguments before '--'.
} /* ignore all unrecognized arguments before '--'. */
}
src = llist_init();

2
src/GRANULAR/pair_gran_hertz_history.cpp
View File

@ -87,7 +87,6 @@ void PairGranHertzHistory::compute(int eflag, int vflag)
double **torque = atom->torque;
double *radius = atom->radius;
double *rmass = atom->rmass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
@ -367,7 +366,6 @@ double PairGranHertzHistory::single(int i, int j, int itype, int jtype,
// if I or J is frozen, meff is other particle
double *rmass = atom->rmass;
int *type = atom->type;
int *mask = atom->mask;
mi = rmass[i];

2
src/GRANULAR/pair_gran_hooke.cpp
View File

@ -81,7 +81,6 @@ void PairGranHooke::compute(int eflag, int vflag)
double **torque = atom->torque;
double *radius = atom->radius;
double *rmass = atom->rmass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
@ -285,7 +284,6 @@ double PairGranHooke::single(int i, int j, int itype, int jtype, double rsq,
// if I or J is frozen, meff is other particle
double *rmass = atom->rmass;
int *type = atom->type;
int *mask = atom->mask;
mi = rmass[i];

2
src/GRANULAR/pair_gran_hooke_history.cpp
View File

@ -129,7 +129,6 @@ void PairGranHookeHistory::compute(int eflag, int vflag)
double **torque = atom->torque;
double *radius = atom->radius;
double *rmass = atom->rmass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
@ -670,7 +669,6 @@ double PairGranHookeHistory::single(int i, int j, int itype, int jtype,
// if I or J is frozen, meff is other particle
double *rmass = atom->rmass;
int *type = atom->type;
int *mask = atom->mask;
mi = rmass[i];

8
src/KOKKOS/Install.sh
View File

@ -189,6 +189,14 @@ if (test $1 = 1) then
sed -i -e '5 i \include ..\/..\/lib\/kokkos\/Makefile.kokkos' ../Makefile.package.settings
fi
# comb/omp triggers a persistent bug in nvcc. deleting it.
rm -f ../*_comb_omp.*
elif (test $1 = 2) then
# comb/omp triggers a persistent bug in nvcc. deleting it.
rm -f ../*_comb_omp.*
elif (test $1 = 0) then
if (test -e ../Makefile.package) then

1
src/KOKKOS/fix_nh_kokkos.cpp
View File

@ -291,7 +291,6 @@ void FixNHKokkos<DeviceType>::final_integrate()
template<class DeviceType>
void FixNHKokkos<DeviceType>::remap()
{
int i;
double oldlo,oldhi;
double expfac;

1
src/MANYBODY/pair_airebo.cpp
View File

@ -2251,7 +2251,6 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
ril[1] = rij[1]+rjl[1];
ril[2] = rij[2]+rjl[2];
ril2 = (ril[0]*ril[0])+(ril[1]*ril[1])+(ril[2]*ril[2]);
rijrjl = 2.0*rijmag*rjlmag;
rjl2 = rjlmag*rjlmag;
costmp = 0.5*(rij2+rjl2-ril2)/rijmag/rjlmag;
tspijl = Sp2(costmp,thmin,thmax,dtsijl);

8
src/MANYBODY/pair_bop.cpp
View File

@ -993,7 +993,6 @@ void PairBOP::theta()
int *ilist;
int *iilist;
int **firstneigh;
int maxn,maxt;
double rj2,rk2,rsq,ps;
double rj1k1,rj2k2;
double **x = atom->x;
@ -1015,8 +1014,6 @@ void PairBOP::theta()
itype = map[type[i]]+1;
iilist=firstneigh[i];
maxt=0;
maxn=0;
nlisti=BOP_total[i];
for(jj=0;jj<nlisti;jj++) {
temp_ij=BOP_index[i]+jj;
@ -1038,10 +1035,8 @@ void PairBOP::theta()
+disij[1][temp_ij]*disij[1][temp_ij]
+disij[2][temp_ij]*disij[2][temp_ij];
rij[temp_ij]=sqrt(rsq);
if(rij[temp_ij]<=rcut[i12]) {
if(rij[temp_ij]<=rcut[i12])
neigh_flag[temp_ij]=1;
maxt++;
}
else
neigh_flag[temp_ij]=0;
if(rij[temp_ij]<=rcut3[i12])
@ -1067,7 +1062,6 @@ void PairBOP::theta()
dRepul[temp_ij]=(pRepul6[i12][ks-1]*ps+pRepul5[i12][ks-1])*ps
+pRepul4[i12][ks-1];
}
if(maxt>maxn) maxn=maxt;
}
for (ii = 0; ii < nall; ii++) {
n=0;

54
src/MANYBODY/pair_eim.cpp
View File

@ -921,13 +921,13 @@ int PairEIM::grabsingle(FILE *fptr, int i)
pch1 = strstr(pch1,"element:");
if (pch1 != NULL) {
pch2 = strtok(NULL, " \t\n\r\f");
if (pch2 != NULL) data = strtok (NULL, "?");
if (strcmp(pch2,elements[i]) == 0) {
sscanf(data,"%d %lg %lg %lg %lg %lg %lg",&setfl->ielement[i],
&setfl->mass[i],&setfl->negativity[i],&setfl->ra[i],
&setfl->ri[i],&setfl->Ec[i],&setfl->q0[i]);
} else {
pch2 = NULL;
if (pch2 != NULL) {
data = strtok (NULL, "?");
if (strcmp(pch2,elements[i]) == 0) {
sscanf(data,"%d %lg %lg %lg %lg %lg %lg",&setfl->ielement[i],
&setfl->mass[i],&setfl->negativity[i],&setfl->ra[i],
&setfl->ri[i],&setfl->Ec[i],&setfl->q0[i]);
} else pch2 = NULL;
}
}
}
@ -960,25 +960,27 @@ int PairEIM::grabpair(FILE *fptr, int i, int j)
pch2 = strtok (NULL, " \t\n\r\f");
if (pch2 != NULL) pch3 = strtok (NULL, " \t\n\r\f");
if (pch3 != NULL) data = strtok (NULL, "?");
if ((strcmp(pch2,elements[i]) == 0 &&
strcmp(pch3,elements[j]) == 0) ||
(strcmp(pch2,elements[j]) == 0 &&
strcmp(pch3,elements[i]) == 0)) {
sscanf(data,"%lg %lg %lg %lg %lg",
&setfl->rcutphiA[ij],&setfl->rcutphiR[ij],
&setfl->Eb[ij],&setfl->r0[ij],&setfl->alpha[ij]);
fgets(line,MAXLINE,fptr);
sscanf(line,"%lg %lg %lg %lg %lg",
&setfl->beta[ij],&setfl->rcutq[ij],&setfl->Asigma[ij],
&setfl->rq[ij],&setfl->rcutsigma[ij]);
fgets(line,MAXLINE,fptr);
sscanf(line,"%lg %lg %lg %d",
&setfl->Ac[ij],&setfl->zeta[ij],&setfl->rs[ij],
&setfl->tp[ij]);
} else {
pch1 = NULL;
pch2 = NULL;
pch3 = NULL;
if ((pch2 != NULL) && (pch3 != NULL)) {
if ((strcmp(pch2,elements[i]) == 0 &&
strcmp(pch3,elements[j]) == 0) ||
(strcmp(pch2,elements[j]) == 0 &&
strcmp(pch3,elements[i]) == 0)) {
sscanf(data,"%lg %lg %lg %lg %lg",
&setfl->rcutphiA[ij],&setfl->rcutphiR[ij],
&setfl->Eb[ij],&setfl->r0[ij],&setfl->alpha[ij]);
fgets(line,MAXLINE,fptr);
sscanf(line,"%lg %lg %lg %lg %lg",
&setfl->beta[ij],&setfl->rcutq[ij],&setfl->Asigma[ij],
&setfl->rq[ij],&setfl->rcutsigma[ij]);
fgets(line,MAXLINE,fptr);
sscanf(line,"%lg %lg %lg %d",
&setfl->Ac[ij],&setfl->zeta[ij],&setfl->rs[ij],
&setfl->tp[ij]);
} else {
pch1 = NULL;
pch2 = NULL;
pch3 = NULL;
}
}
}
}

2
src/MANYBODY/pair_polymorphic.cpp
View File

@ -631,6 +631,8 @@ void PairPolymorphic::read_file(char *file)
if (ptr) maxX = atof(ptr);
if (ptr == NULL)
error->all(FLERR,"Potential file incompatible with this pair style version");
if ((ng == 0) || (nr == 0) || (nx == 0))
error->all(FLERR,"Error reading potential file header");
npair = nelements*(nelements+1)/2;
ntriple = nelements*nelements*nelements;

2
src/MEAM/pair_meam.cpp
View File

@ -555,7 +555,7 @@ void PairMEAM::read_files(char *globalfile, char *userfile)
for (i = 0; i < nelements; i++)
if (strcmp(words[0],elements[i]) == 0) break;
if (i == nelements) continue;
if (i >= nelements) continue;
// skip if element already appeared

216
src/Make.py
View File

@ -15,14 +15,14 @@ import sys,os,commands,re,copy,subprocess
# setargs = makefile settings
# actionargs = allowed actions (also lib-dir and machine)
abbrevs = "adhjmoprsv"
abbrevs = "adhjmoprsvz"
switchclasses = ("actions","dir","help","jmake","makefile",
"output","packages","redo","settings","verbose")
"output","packages","redo","settings","verbose","zoutput")
libclasses = ("atc","awpmd","colvars","cuda","gpu","h5md",
"meam","poems","python","qmmm","reax","voronoi")
buildclasses = ("intel","kokkos")
makeclasses = ("cc","mpi","fft","jpg","png")
makeclasses = ("cc","flags","mpi","fft","jpg","png")
setargs = ("gzip","#gzip","ffmpeg","#ffmpeg","smallbig","bigbig","smallsmall")
actionargs = ("lib-all","file","clean","exe")
@ -137,27 +137,37 @@ class Actions:
lib-all builds all auxiliary libs needed by installed packages
lib-dir builds a specific lib whether package installed or not
dir is any dir in lib directory (atc, cuda, meam, etc) except linalg
(2) file = create src/MAKE/MINE/Makefile.auto
use -m switch for Makefile.machine to start from,
else use existing Makefile.auto
adds settings needed for installed accelerator packages
existing Makefile.auto is NOT changed unless "file" action is specified
(2) file = create a new src/MAKE/MINE/Makefile.auto
if file not specified, existing Makefile.auto is NOT changed
except by -m switch, which will copy Makefile.machine to Makefile.auto
note that exe action can add an -m switch, as described below
if file is specified, new Makefile.auto is created
if "-m machine" specified (or added by exe),
start with existing Makefile.machine, else existing Makefile.auto
if "-m none" specified, start Makefile.auto from scratch
must use -cc and -mpi switches to specify compiler and MPI
settings for these switches will alter Makefile.auto
-s, -intel, -kokkos, -cc, -mpi, -fft, -jpg, -png
if these accelerator packages are installed, they induce settings
that will alter Makefile.auto: opt, user-omp, user-intel, kokkos
use -z switch to copy final Makefile.auto to new filename
(3) clean = invoke "make clean-auto" to insure clean build on current files
useful if compiler flags have changed
(4) exe or machine = build LAMMPS
machine can be any existing Makefile.machine suffix
machine is converted to "exe" action, as well as:
machine is converted to "exe" action, and additionally:
"-m machine" is added if -m switch is not specified
"-o machine" is added if -o switch is not specified
if either "-m" or "-o" are specified, they are not overridden
does not invoke any lib builds, since libs could be previously built
exe always builds using src/MAKE/MINE/Makefile.auto
if file action also specified, it creates Makefile.auto
exe ALWAYS builds using src/MAKE/MINE/Makefile.auto
if file action also specified, it creates a new Makefile.auto
else if -m switch specified,
existing Makefile.machine is copied to create Makefile.auto
else Makefile.auto must already exist and is not changed
produces src/lmp_auto, or error message if unsuccessful
build produces src/lmp_auto, or error message if unsuccessful
use -o switch to copy src/lmp_auto to new filename
use -z switch to copy src/MAKE/MINE/Makefile.auto to new filename
"""
def check(self):
@ -177,7 +187,7 @@ class Actions:
cleans.append(one)
elif one == "exe":
exes.append(one)
# one action can be unknown in case is a machine (checked in setup)
# one action can be unknown, must be a machine (checked in setup)
else:
exes.append(one)
if len(set(libs)) != len(libs) or \
@ -236,9 +246,9 @@ class Actions:
def file(self,caller):
# if caller = "file", create from mpi or read from makefile.machine or auto
# if caller = "exe" and "file" action already invoked, read from auto
# if caller = "exe" and no "file" action, read from makefile.machine or auto
# if caller="file", create from mpi or read from Makefile.machine or auto
# if caller="exe" and "file" action already invoked, read from auto
# if caller="exe" and no "file" action, read from Makefile.machine or auto
if caller == "file":
if makefile and makefile.machine == "none":
@ -279,7 +289,7 @@ class Actions:
make.addvar("CC","-cxx=%s" % wrapper)
make.addvar("LINK","-cxx=%s" % wrapper)
elif "-lmpi" in txt:
make.addvar("OMPI_CXX",wrapper,"cc")
make.addvar("export OMPI_CXX",wrapper,"cc")
precompiler = "env OMPI_CXX=%s " % wrapper
else: error("Could not add MPI wrapper compiler, " +
"did not recognize OpenMPI or MPICH")
@ -287,8 +297,20 @@ class Actions:
make.addvar("CCFLAGS","-O3")
make.setvar("LINKFLAGS","-g")
make.addvar("LINKFLAGS","-O")
# add CC and LINK flags
# add MPI settings
if flags:
for flag in flags.CC:
flag = "-" + flag
if flag[:2] == "-O": make.delvar("CCFLAGS","-O*")
make.addvar("CCFLAGS",flag)
for flag in flags.LINK:
flag = "-" + flag
if flag[:2] == "-O": make.delvar("LINKFLAGS","-O*")
make.addvar("LINKFLAGS",flag)
# add MPI settings
if mpi:
make.delvar("MPI_INC","*")
@ -397,7 +419,7 @@ class Actions:
make.addvar("KOKKOS_DEVICES","OpenMP","lmp")
make.addvar("KOKKOS_ARCH","KNC","lmp")
# add LMP settings
# add LMP_INC ifdef settings
if settings:
list = settings.inlist
@ -465,12 +487,13 @@ class Actions:
# set self.stubs if Makefile.auto uses STUBS lib in MPI settings
if "-lmpi_stubs" in make.getvar("MPI_LIB"): self.stubs = 1
if make.getvar("MPI_LIB") and "-lmpi_stubs" in make.getvar("MPI_LIB"):
self.stubs = 1
else: self.stubs = 0
# write out Makefile.auto
# unless caller = "exe" and "file" action already invoked
if caller == "file" or "file" not in self.alist:
make.write("%s/MAKE/MINE/Makefile.auto" % dir.src,1)
print "Created src/MAKE/MINE/Makefile.auto"
@ -510,13 +533,23 @@ class Actions:
print txt
error('Unsuccessful "make stubs"')
print "Created src/STUBS/libmpi_stubs.a"
if jmake: str = "cd %s; make -j %d auto" % (dir.src,jmake.n)
else: str = "cd %s; make auto" % dir.src
# special hack for shannon GPU cluster
# must use "srun make" if on it and building w/ GPU package, else just make
# this is b/c Cuda libs are not all available on host
make = "make"
if "shannon" in os.environ.get("HOST") and packages.final["gpu"]:
make = "srun make"
if jmake: str = "cd %s; %s -j %d auto" % (dir.src,make,jmake.n)
else: str = "cd %s; %s auto" % (dir.src,make)
# if verbose, print output as build proceeds, else only print if fails
if verbose: subprocess.call(str,shell=True)
else:
print str
try: subprocess.check_output(str,stderr=subprocess.STDOUT,shell=True)
except Exception as e: print e.output
@ -574,8 +607,8 @@ Syntax: Make.py switch args ...
list one or more actions, in any order
machine is a Makefile.machine suffix
one-letter switches:
-d (dir), -j (jmake), -m (makefile), -o (output),
-p (packages), -r (redo), -s (settings), -v (verbose)
-d (dir), -j (jmake), -m (makefile), -o (output), -p (packages),
-r (redo), -s (settings), -v (verbose), -z (makefile output)
switches for libs:
-atc, -awpmd, -colvars, -cuda, -gpu, -h5md,
-meam, -poems, -python, -qmmm, -reax, -voronoi
@ -898,9 +931,13 @@ class Settings:
def help(self):
return """
-s set1 set2 ...
possible settings = gzip smallbig bigbig smallsmall
add each setting as LAMMPS setting to created Makefile.auto
if -s not specified, no settings are changed in Makefile.auto
possible settings = gzip #gzip ffmpeg #ffmpeg smallbig bigbig smallsmall
alter LAMMPS ifdef settings in Makefile.auto
only happens if new Makefile.auto is created by use of "file" action
gzip and #gzip turn on/off LAMMPS_GZIP setting
ffmpeg and #ffmpeg turn on/off LAMMPS_FFMPEG setting
smallbig, bigbig, smallsmall turn on LAMMPS_SMALLBIG, etc
and turn off other two
"""
def check(self):
@ -924,6 +961,23 @@ class Verbose:
def check(self):
if len(self.inlist): error("-v args are invalid")
# zoutput switch for making copy of final Makefile.auto
class Zoutput:
def __init__(self,list):
self.inlist = copy.copy(list)
def help(self):
return """
-z machine
copy created/used src/MAKE/MINE/Makefile.auto to Makefile.machine in same dir
this can be used to preserve the machine makefile
"""
def check(self):
if len(self.inlist) != 1: error("-z args are invalid")
self.machine = self.inlist[0]
# ----------------------------------------------------------------
# lib classes, one per LAMMPS auxiliary lib
# ----------------------------------------------------------------
@ -1087,15 +1141,15 @@ class CUDA:
def __init__(self,list):
self.inlist = copy.copy(list)
self.mode = "double"
self.arch = "31"
self.arch = "35"
def help(self):
return """
-cuda mode=double arch=31
-cuda mode=double arch=35
all args are optional and can be in any order
mode = double or mixed or single (def = double)
arch = M (def = 31)
M = 31 for Kepler
arch = M (def = 35)
M = 31,35,37,etc for Kepler
M = 20 for CC2.0 (GF100/110, e.g. C2050,GTX580,GTX470)
M = 21 for CC2.1 (GF104/114, e.g. GTX560, GTX460, GTX450)
M = 13 for CC1.3 (GF200, e.g. C1060, GTX285)
@ -1144,16 +1198,18 @@ class GPU:
def __init__(self,list):
self.inlist = copy.copy(list)
self.make = "linux.double"
self.lammpsflag = self.modeflag = self.archflag = 0
self.lammpsflag = self.modeflag = self.archflag = self.homeflag = 0
def help(self):
return """
-gpu make=suffix lammps=suffix2 mode=double arch=N
-gpu make=suffix lammps=suffix2 mode=double arch=N home=path
all args are optional and can be in any order
make = use Makefile.suffix (def = linux.double)
lammps = use Makefile.lammps.suffix2 (def = EXTRAMAKE in makefile)
mode = double or mixed or single (def = CUDA_PREC in makefile)
arch = 31 (Kepler) or 21 (Fermi) (def = CUDA_ARCH in makefile)
arch = 3x (x = digit for Kepler) or 2x (x = digit for Fermi)
(def = CUDA_ARCH in makefile)
home = path to Cuda, e.g. /usr/local/cuda (def = CUDA_HOME in makefile)
"""
def check(self):
@ -1172,6 +1228,9 @@ class GPU:
elif words[0] == "arch":
self.arch = words[1]
self.archflag = 1
elif words[0] == "home":
self.home = words[1]
self.homeflag = 1
else: error("-gpu args are invalid")
if self.modeflag and (self.mode != "double" and
self.mode != "mixed" and
@ -1192,13 +1251,22 @@ class GPU:
make.setvar("CUDA_PRECISION","-D_SINGLE_SINGLE")
if self.archflag:
make.setvar("CUDA_ARCH","-arch=sm_%s" % self.arch)
if self.homeflag:
make.setvar("CUDA_HOME",self.home)
if self.lammpsflag:
make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)
make.write("%s/Makefile.auto" % libdir)
commands.getoutput("cd %s; make -f Makefile.auto clean" % libdir)
if jmake: str = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
else: str = "cd %s; make -f Makefile.auto" % libdir
# special hack for shannon GPU cluster
# must use "srun make" if on it, else just make
# this is b/c Cuda libs are not all available on host
make = "make"
if "shannon" in os.environ.get("HOST"): make = "srun make"
commands.getoutput("cd %s; %s -f Makefile.auto clean" % (libdir,make))
if jmake: str = "cd %s; %s -j %d -f Makefile.auto" % (libdir,make,jmake.n)
else: str = "cd %s; %s -f Makefile.auto" % (libdir,make)
# if verbose, print output as build proceeds, else only print if fails
@ -1574,14 +1642,16 @@ class Kokkos:
mode is not optional, arch is optional
mode = omp or cuda or phi (def = KOKKOS_DEVICES setting in Makefile )
build Kokkos package for omp or cuda or phi
set KOKKOS_DEVICES to "OpenMP" (omp, phi) or "Cuda, OpenMP" (cuda)
arch = 31 (Kepler) or 21 (Fermi) (def = -arch setting in Makefile)
sets KOKKOS_DEVICES to "OpenMP" (omp, phi) or "Cuda, OpenMP" (cuda)
arch = number like 35 (Kepler) or 21 (Fermi)
sets KOKKOS_ARCH to appropriate value
"""
def check(self):
print self.inlist
if self.inlist != None and len(self.inlist) == 0:
error("-kokkos args are invalid")
if self.inlist == None: return
if len(self.inlist) < 1: error("-kokkos args are invalid")
self.mode = self.inlist[0]
@ -1596,7 +1666,7 @@ class Kokkos:
else: error("-kokkos args are invalid")
# ----------------------------------------------------------------
# makefile classes for CC, MPI, JPG, PNG, FFT settings
# makefile classes for CC, FLAGS, MPI, JPG, PNG, FFT settings
# ----------------------------------------------------------------
# Cc class
@ -1610,7 +1680,8 @@ class Cc:
def help(self):
return """
-cc compiler wrap=wcompiler
change CC setting in makefile
alter CC setting in Makefile.auto
only happens if new Makefile.auto is created by use of "file" action
compiler is required, all other args are optional
compiler = any string with g++ or icc or icpc
or mpi (or mpicxx, mpiCC, mpiicpc, etc)
@ -1644,6 +1715,41 @@ class Cc:
self.wrap = words[1]
else: error("-cc args are invalid")
# Flags class
class Flags:
def __init__(self,list):
self.inlist = copy.copy(list)
self.CC = []
self.LINK = []
def help(self):
return """
-flags flag f1 f2 ... flag f1 f2 ...
alter CCFLAGS or LINKFLAGS settings in Makefile.auto
only happens if new Makefile.auto is created by use of "file" action
flag = CC or LINK
one or both can be specified
f1,f2,etc = flag to add or replace
"-" char will be prepended to each
for example: g, O3, xHost, "fp-model fast=2"
will become: -g, -O3, -xHost, -fp-model fast=2
for -O,-O2,-O3,etc: existing -O* will first be removed
"""
def check(self):
if len(self.inlist) < 1: error("-flags args are invalid")
self.CC = [] # necessary?
self.LINK = []
mode = ""
for one in self.inlist:
if one == "CC": mode = "CC"
elif one == "LINK": mode = "LINK"
else:
if not mode: error("-flags args are invalid")
if mode == "CC": self.CC.append(one)
elif mode == "LINK": self.LINK.append(one)
# Mpi class
class Mpi:
@ -1654,7 +1760,8 @@ class Mpi:
def help(self):
return """
-mpi style dir=path
change MPI settings in makefile
alter MPI settings in Makefile.auto
only happens if new Makefile.auto is created by use of "file" action
style is required, all other args are optional
style = mpi or mpich or ompi or serial
mpi = no MPI settings (assume compiler is MPI wrapper)
@ -1687,9 +1794,10 @@ class Fft:
def help(self):
return """
-fft mode lib=libname dir=homedir idir=incdir ldir=libdir
change FFT settings in makefile
alter FFT settings in Makefile.auto
only happens if new Makefile.auto is created by use of "file" action
mode is required, all other args are optional
removes all current FFT variable settings
first removes all current FFT variable settings
mode = none or fftw or fftw3 or ...
adds -DFFT_MODE setting
lib = name of FFT library to link with (def is libname = mode)
@ -1727,6 +1835,8 @@ class Jpg:
def help(self):
return """
-jpg flag dir=homedir idir=incdir ldir=libdir
alter JPG settings in Makefile.auto
only happens if new Makefile.auto is created by use of "file" action
change JPG settings in makefile
all args are optional, flag must come first if specified
flag = yes or no (def = yes)
@ -1764,7 +1874,8 @@ class Png:
def help(self):
return """
-png flag dir=homedir idir=incdir ldir=libdir
change PNG settings in makefile
alter PNG settings in Makefile.auto
only happens if new Makefile.auto is created by use of "file" action
all args are optional, flag must come first if specified
flag = yes or no (def = yes)
include or exclude PNG support
@ -2143,13 +2254,22 @@ while 1:
packages.uninstall()
# create output file if requested and exe action performed
# create copy of executable if requested, and exe action performed
if output and actions and "exe" in actions.alist:
txt = "cp %s/lmp_auto %s/lmp_%s" % (dir.src,dir.cwd,output.machine)
commands.getoutput(txt)
print "Created lmp_%s in %s" % (output.machine,dir.cwd)
# create copy of Makefile.auto if requested, and file or exe action performed
if zoutput and actions and \
("file" in actions.alist or "exe" in actions.alist):
txt = "cp %s/MAKE/MINE/Makefile.auto %s/MAKE/MINE/Makefile.%s" % \
(dir.src,dir.src,zoutput.machine)
commands.getoutput(txt)
print "Created Makefile.%s in %s/MAKE/MINE" % (zoutput.machine,dir.src)
# write current Make.py command to src/Make.py.last
fp = open("%s/Make.py.last" % dir.src,'w')

4
src/Makefile
View File

@ -205,8 +205,8 @@ install-python:
tar:
@cd STUBS; $(MAKE) clean
@cd ..; tar cvzf src/$(ROOT)_src.tar.gz \
src/Make* src/Package.sh src/Depend.sh \
src/MAKE src/*.cpp src/*.h src/STUBS \
src/Make* src/Package.sh src/Depend.sh src/Install.sh \
src/MAKE src/DEPEND src/*.cpp src/*.h src/STUBS \
$(patsubst %,src/%,$(PACKAGEUC)) $(patsubst %,src/%,$(PACKUSERUC)) \
--exclude=*/.svn
@cd STUBS; $(MAKE)

9
src/QEQ/fix_qeq_fire.cpp
View File

@ -107,17 +107,16 @@ void FixQEqFire::init()
void FixQEqFire::pre_force(int vflag)
{
int inum, *ilist;
int i,ii,iloop,loopmax;
int *mask = atom->mask;
int i,ii,iloop;
double *q = atom->q;
double vmax,vdotf,vdotfall,vdotv,vdotvall,fdotf,fdotfall;
double scale1,scale2;
double dtvone,dtv;
double enegtot,enegchk,enegmax;
double enegtot,enegchk;
double alpha = qdamp;
double dt, dtmax;
double enegchkall,enegmaxall;
double enegchkall;
bigint ntimestep = update->ntimestep;
bigint last_negative = 0;
@ -225,7 +224,7 @@ void FixQEqFire::pre_force(int vflag)
if (comm->me == 0) {
if (iloop == maxiter) {
char str[128];
sprintf(str,"Charges did not converge at step "BIGINT_FORMAT
sprintf(str,"Charges did not converge at step " BIGINT_FORMAT
": %lg",update->ntimestep,enegchk);
error->warning(FLERR,str);
}

31
src/REPLICA/temper.cpp
View File

@ -93,13 +93,38 @@ void Temper::command(int narg, char **arg)
if (nswaps*nevery != nsteps)
error->universe_all(FLERR,"Non integer # of swaps in temper command");
// fix style must be appropriate for temperature control
// fix style must be appropriate for temperature control, i.e. it needs
// to provide a working Fix::reset_target() and must not change the volume.
if ((strcmp(modify->fix[whichfix]->style,"nvt") != 0) &&
(strcmp(modify->fix[whichfix]->style,"nvt/asphere") != 0) &&
(strcmp(modify->fix[whichfix]->style,"nvt/asphere/omp") != 0) &&
(strcmp(modify->fix[whichfix]->style,"nvt/body") != 0) &&
(strcmp(modify->fix[whichfix]->style,"nvt/eff") != 0) &&
(strcmp(modify->fix[whichfix]->style,"nvt/intel") != 0) &&
(strcmp(modify->fix[whichfix]->style,"nvt/kk") != 0) &&
(strcmp(modify->fix[whichfix]->style,"nvt/kk/host") != 0) &&
(strcmp(modify->fix[whichfix]->style,"nvt/kk/device") != 0) &&
(strcmp(modify->fix[whichfix]->style,"nvt/omp") != 0) &&
(strcmp(modify->fix[whichfix]->style,"nvt/sphere") != 0) &&
(strcmp(modify->fix[whichfix]->style,"nvt/sphere/omp") != 0) &&
(strcmp(modify->fix[whichfix]->style,"langevin") != 0) &&
(strcmp(modify->fix[whichfix]->style,"langevin/drude") != 0) &&
(strcmp(modify->fix[whichfix]->style,"langevin/eff") != 0) &&
(strcmp(modify->fix[whichfix]->style,"gld") != 0) &&
(strcmp(modify->fix[whichfix]->style,"gle") != 0) &&
(strcmp(modify->fix[whichfix]->style,"rigid/nvt") != 0) &&
(strcmp(modify->fix[whichfix]->style,"rigid/nvt/small") != 0) &&
(strcmp(modify->fix[whichfix]->style,"rigid/nvt/omp") != 0) &&
(strcmp(modify->fix[whichfix]->style,"rigid/nvt/small/omp") != 0) &&
(strcmp(modify->fix[whichfix]->style,"temp/berendsen") != 0) &&
(strcmp(modify->fix[whichfix]->style,"temp/rescale") != 0))
error->universe_all(FLERR,"Tempering temperature fix is not valid");
(strcmp(modify->fix[whichfix]->style,"temp/berendsen/cuda") != 0) &&
(strcmp(modify->fix[whichfix]->style,"temp/csvr") != 0) &&
(strcmp(modify->fix[whichfix]->style,"temp/csld") != 0) &&
(strcmp(modify->fix[whichfix]->style,"temp/rescale") != 0) &&
(strcmp(modify->fix[whichfix]->style,"temp/rescale/cuda") != 0) &&
(strcmp(modify->fix[whichfix]->style,"temp/rescale/eff") != 0))
error->universe_all(FLERR,"Tempering temperature fix is not supported");
// setup for long tempering run

2
src/STUBS/Makefile.mingw32-cross
View File

@ -16,7 +16,7 @@ OBJ = $(SRC:%.c=%_mingw32.o)
# System-specific settings
CC = i686-w64-mingw32-gcc
CCFLAGS = -O2 -Wall -march=i686 -mtune=generic -mfpmath=387 -mpc64
CCFLAGS = -O2 -Wall -march=i686 -mtune=generic -mfpmath=387 -mpc64 -I.
ARCHIVE = i686-w64-mingw32-ar
ARCHFLAG = rs

2
src/STUBS/Makefile.mingw64-cross
View File

@ -16,7 +16,7 @@ OBJ = $(SRC:%.c=%_mingw64.o)
# System-specific settings
CC = x86_64-w64-mingw32-gcc
CCFLAGS = -O2 -Wall -march=core2 -mtune=core2 -msse2 -mpc64
CCFLAGS = -O2 -Wall -march=core2 -mtune=core2 -msse2 -mpc64 -I.
ARCHIVE = x86_64-w64-mingw32-ar
ARCHFLAG = rs

1
src/USER-OMP/pair_airebo_omp.cpp
View File

@ -1097,7 +1097,6 @@ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double rij[3], double rijmag
ril[1] = rij[1]+rjl[1];
ril[2] = rij[2]+rjl[2];
ril2 = (ril[0]*ril[0])+(ril[1]*ril[1])+(ril[2]*ril[2]);
rijrjl = 2.0*rijmag*rjlmag;
rjl2 = rjlmag*rjlmag;
costmp = 0.5*(rij2+rjl2-ril2)/rijmag/rjlmag;
tspijl = Sp2(costmp,thmin,thmax,dtsijl);

2
src/compute_chunk_atom.cpp
View File

@ -398,7 +398,7 @@ ComputeChunkAtom::ComputeChunkAtom(LAMMPS *lmp, int narg, char **arg) :
double scale;
if (which == BIN1D || which == BIN2D || which == BIN3D ||
which == BINCYLINDER) {
if (which == BIN1D || BINCYLINDER) ndim = 1;
if (which == BIN1D || which == BINCYLINDER) ndim = 1;
if (which == BIN2D) ndim = 2;
if (which == BIN3D) ndim = 3;
for (int idim = 0; idim < ndim; idim++) {

13
src/domain.cpp
View File

@ -503,13 +503,12 @@ void Domain::pbc()
double *coord;
int n3 = 3*nlocal;
if (x) {
coord = &x[0][0];
int flag = 0;
for (i = 0; i < n3; i++)
if (!ISFINITE(*coord++)) flag = 1;
if (flag) error->one(FLERR,"Non-numeric atom coords - simulation unstable");
}
coord = &x[0][0]; // note: x is always initialzed to at least one element.
int flag = 0;
for (i = 0; i < n3; i++)
if (!ISFINITE(*coord++)) flag = 1;
if (flag) error->one(FLERR,"Non-numeric atom coords - simulation unstable");
// setup for PBC checks
if (triclinic == 0) {

1
src/dump_image.cpp
View File

@ -850,7 +850,6 @@ void DumpImage::create_image()
if (bodyflag) {
Body *bptr = avec_body->bptr;
double **x = atom->x;
int *body = atom->body;
m = 0;

3
src/fix_ave_time.cpp
View File

@ -23,7 +23,6 @@
#include "force.h"
#include "modify.h"
#include "compute.h"
#include "group.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
@ -55,6 +54,8 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
global_freq = nfreq;
dynamic_group_allow = 1;
// scan values to count them
// then read options so know mode = SCALAR/VECTOR before re-reading values

1
src/math_const.h
View File

@ -25,6 +25,7 @@ namespace MathConst {
static const double MY_PI2 = 1.57079632679489661923; // pi/2
static const double MY_PI4 = 0.78539816339744830962; // pi/4
static const double MY_PIS = 1.77245385090551602729; // sqrt(pi)
static const double MY_ISPI4 = 1.12837916709551257389; // 1/sqrt(pi/4)
static const double MY_SQRT2 = 1.41421356237309504880; // sqrt(2)
static const double MY_CBRT2 = 1.25992104989487316476; // 2*(1/3)
}

2
src/read_data.cpp
View File

@ -1468,7 +1468,7 @@ void ReadData::bonus(bigint nbonus, AtomVec *ptr, const char *type)
void ReadData::bodies(int firstpass)
{
int i,m,nchunk,nline,nmax,ninteger,ndouble,nword,ncount,onebody,tmp;
int m,nchunk,nline,nmax,ninteger,ndouble,nword,ncount,onebody,tmp;
char *eof;
int mapflag = 0;

1
src/set.cpp
View File

@ -917,7 +917,6 @@ void Set::setrandom(int keyword)
} else if (keyword == THETA_RANDOM) {
int nlocal = atom->nlocal;
double theta;
for (i = 0; i < nlocal; i++) {
if (select[i]) {
if (atom->line[i] < 0)