forked from lijiext/lammps
Merge pull request #598 from akohlmey/last-minute-changes
last minute changes for stable release
This commit is contained in:
sjplimp
GitHub
commit
2806f070a4
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@ -1,82 +0,0 @@
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|||
#!/usr/bin/env python
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||||
|
||||
# install.py tool to do a generic build of a library
|
||||
# soft linked to by many of the lib/Install.py files
|
||||
# used to automate the steps described in the corresponding lib/README
|
||||
|
||||
import sys,commands,os
|
||||
|
||||
# help message
|
||||
|
||||
help = """
|
||||
Syntax: python Install.py -m machine -e suffix
|
||||
specify -m and optionally -e, order does not matter
|
||||
-m = peform a clean followed by "make -f Makefile.machine"
|
||||
machine = suffix of a lib/Makefile.* file
|
||||
-e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
|
||||
does not alter existing Makefile.machine
|
||||
"""
|
||||
|
||||
# print error message or help
|
||||
|
||||
def error(str=None):
|
||||
if not str: print help
|
||||
else: print "ERROR",str
|
||||
sys.exit()
|
||||
|
||||
# parse args
|
||||
|
||||
args = sys.argv[1:]
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||||
nargs = len(args)
|
||||
if nargs == 0: error()
|
||||
|
||||
machine = None
|
||||
extraflag = 0
|
||||
|
||||
iarg = 0
|
||||
while iarg < nargs:
|
||||
if args[iarg] == "-m":
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||||
if iarg+2 > nargs: error()
|
||||
machine = args[iarg+1]
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||||
iarg += 2
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||||
elif args[iarg] == "-e":
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if iarg+2 > nargs: error()
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||||
extraflag = 1
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suffix = args[iarg+1]
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iarg += 2
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else: error()
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||||
|
||||
# set lib from working dir
|
||||
|
||||
cwd = os.getcwd()
|
||||
lib = os.path.basename(cwd)
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||||
|
||||
# create Makefile.auto as copy of Makefile.machine
|
||||
# reset EXTRAMAKE if requested
|
||||
|
||||
if not os.path.exists("Makefile.%s" % machine):
|
||||
error("lib/%s/Makefile.%s does not exist" % (lib,machine))
|
||||
|
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lines = open("Makefile.%s" % machine,'r').readlines()
|
||||
fp = open("Makefile.auto",'w')
|
||||
|
||||
for line in lines:
|
||||
words = line.split()
|
||||
if len(words) == 3 and extraflag and \
|
||||
words[0] == "EXTRAMAKE" and words[1] == '=':
|
||||
line = line.replace(words[2],"Makefile.lammps.%s" % suffix)
|
||||
print >>fp,line,
|
||||
|
||||
fp.close()
|
||||
|
||||
# make the library via Makefile.auto
|
||||
|
||||
print "Building lib%s.a ..." % lib
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cmd = "make -f Makefile.auto clean; make -f Makefile.auto"
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txt = commands.getoutput(cmd)
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print txt
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||||
|
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if os.path.exists("lib%s.a" % lib): print "Build was successful"
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else: error("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib))
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if not os.path.exists("Makefile.lammps"):
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print "lib/%s/Makefile.lammps was NOT created" % lib
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|
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@ -0,0 +1 @@
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|||
Install.py
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|
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@ -1,82 +0,0 @@
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|||
#!/usr/bin/env python
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||||
|
||||
# install.py tool to do a generic build of a library
|
||||
# soft linked to by many of the lib/Install.py files
|
||||
# used to automate the steps described in the corresponding lib/README
|
||||
|
||||
import sys,commands,os
|
||||
|
||||
# help message
|
||||
|
||||
help = """
|
||||
Syntax: python Install.py -m machine -e suffix
|
||||
specify -m and optionally -e, order does not matter
|
||||
-m = peform a clean followed by "make -f Makefile.machine"
|
||||
machine = suffix of a lib/Makefile.* file
|
||||
-e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
|
||||
does not alter existing Makefile.machine
|
||||
"""
|
||||
|
||||
# print error message or help
|
||||
|
||||
def error(str=None):
|
||||
if not str: print help
|
||||
else: print "ERROR",str
|
||||
sys.exit()
|
||||
|
||||
# parse args
|
||||
|
||||
args = sys.argv[1:]
|
||||
nargs = len(args)
|
||||
if nargs == 0: error()
|
||||
|
||||
machine = None
|
||||
extraflag = 0
|
||||
|
||||
iarg = 0
|
||||
while iarg < nargs:
|
||||
if args[iarg] == "-m":
|
||||
if iarg+2 > nargs: error()
|
||||
machine = args[iarg+1]
|
||||
iarg += 2
|
||||
elif args[iarg] == "-e":
|
||||
if iarg+2 > nargs: error()
|
||||
extraflag = 1
|
||||
suffix = args[iarg+1]
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||||
iarg += 2
|
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else: error()
|
||||
|
||||
# set lib from working dir
|
||||
|
||||
cwd = os.getcwd()
|
||||
lib = os.path.basename(cwd)
|
||||
|
||||
# create Makefile.auto as copy of Makefile.machine
|
||||
# reset EXTRAMAKE if requested
|
||||
|
||||
if not os.path.exists("Makefile.%s" % machine):
|
||||
error("lib/%s/Makefile.%s does not exist" % (lib,machine))
|
||||
|
||||
lines = open("Makefile.%s" % machine,'r').readlines()
|
||||
fp = open("Makefile.auto",'w')
|
||||
|
||||
for line in lines:
|
||||
words = line.split()
|
||||
if len(words) == 3 and extraflag and \
|
||||
words[0] == "EXTRAMAKE" and words[1] == '=':
|
||||
line = line.replace(words[2],"Makefile.lammps.%s" % suffix)
|
||||
print >>fp,line,
|
||||
|
||||
fp.close()
|
||||
|
||||
# make the library via Makefile.auto
|
||||
|
||||
print "Building lib%s.a ..." % lib
|
||||
cmd = "make -f Makefile.auto clean; make -f Makefile.auto"
|
||||
txt = commands.getoutput(cmd)
|
||||
print txt
|
||||
|
||||
if os.path.exists("lib%s.a" % lib): print "Build was successful"
|
||||
else: error("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib))
|
||||
if not os.path.exists("Makefile.lammps"):
|
||||
print "lib/%s/Makefile.lammps was NOT created" % lib
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||||
|
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@ -0,0 +1 @@
|
|||
Install.py
|
||||
|
|
@ -1,82 +0,0 @@
|
|||
#!/usr/bin/env python
|
||||
|
||||
# install.py tool to do a generic build of a library
|
||||
# soft linked to by many of the lib/Install.py files
|
||||
# used to automate the steps described in the corresponding lib/README
|
||||
|
||||
import sys,commands,os
|
||||
|
||||
# help message
|
||||
|
||||
help = """
|
||||
Syntax: python Install.py -m machine -e suffix
|
||||
specify -m and optionally -e, order does not matter
|
||||
-m = peform a clean followed by "make -f Makefile.machine"
|
||||
machine = suffix of a lib/Makefile.* file
|
||||
-e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
|
||||
does not alter existing Makefile.machine
|
||||
"""
|
||||
|
||||
# print error message or help
|
||||
|
||||
def error(str=None):
|
||||
if not str: print help
|
||||
else: print "ERROR",str
|
||||
sys.exit()
|
||||
|
||||
# parse args
|
||||
|
||||
args = sys.argv[1:]
|
||||
nargs = len(args)
|
||||
if nargs == 0: error()
|
||||
|
||||
machine = None
|
||||
extraflag = 0
|
||||
|
||||
iarg = 0
|
||||
while iarg < nargs:
|
||||
if args[iarg] == "-m":
|
||||
if iarg+2 > nargs: error()
|
||||
machine = args[iarg+1]
|
||||
iarg += 2
|
||||
elif args[iarg] == "-e":
|
||||
if iarg+2 > nargs: error()
|
||||
extraflag = 1
|
||||
suffix = args[iarg+1]
|
||||
iarg += 2
|
||||
else: error()
|
||||
|
||||
# set lib from working dir
|
||||
|
||||
cwd = os.getcwd()
|
||||
lib = os.path.basename(cwd)
|
||||
|
||||
# create Makefile.auto as copy of Makefile.machine
|
||||
# reset EXTRAMAKE if requested
|
||||
|
||||
if not os.path.exists("Makefile.%s" % machine):
|
||||
error("lib/%s/Makefile.%s does not exist" % (lib,machine))
|
||||
|
||||
lines = open("Makefile.%s" % machine,'r').readlines()
|
||||
fp = open("Makefile.auto",'w')
|
||||
|
||||
for line in lines:
|
||||
words = line.split()
|
||||
if len(words) == 3 and extraflag and \
|
||||
words[0] == "EXTRAMAKE" and words[1] == '=':
|
||||
line = line.replace(words[2],"Makefile.lammps.%s" % suffix)
|
||||
print >>fp,line,
|
||||
|
||||
fp.close()
|
||||
|
||||
# make the library via Makefile.auto
|
||||
|
||||
print "Building lib%s.a ..." % lib
|
||||
cmd = "make -f Makefile.auto clean; make -f Makefile.auto"
|
||||
txt = commands.getoutput(cmd)
|
||||
print txt
|
||||
|
||||
if os.path.exists("lib%s.a" % lib): print "Build was successful"
|
||||
else: error("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib))
|
||||
if not os.path.exists("Makefile.lammps"):
|
||||
print "lib/%s/Makefile.lammps was NOT created" % lib
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||||
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@ -0,0 +1 @@
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Install.py
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@ -9,13 +9,13 @@
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#ifndef CH5MD_H
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#define CH5MD_H
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#include "hdf5.h"
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#include <stdbool.h>
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#ifdef __cplusplus
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extern "C" {
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#endif
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#include "hdf5.h"
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#include <stdbool.h>
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#define CH5MD_RANK_ERROR -10
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typedef struct h5md_element_struct {
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|
|
|
|||
|
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@ -1,82 +0,0 @@
|
|||
#!/usr/bin/env python
|
||||
|
||||
# install.py tool to do a generic build of a library
|
||||
# soft linked to by many of the lib/Install.py files
|
||||
# used to automate the steps described in the corresponding lib/README
|
||||
|
||||
import sys,commands,os
|
||||
|
||||
# help message
|
||||
|
||||
help = """
|
||||
Syntax: python Install.py -m machine -e suffix
|
||||
specify -m and optionally -e, order does not matter
|
||||
-m = peform a clean followed by "make -f Makefile.machine"
|
||||
machine = suffix of a lib/Makefile.* file
|
||||
-e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
|
||||
does not alter existing Makefile.machine
|
||||
"""
|
||||
|
||||
# print error message or help
|
||||
|
||||
def error(str=None):
|
||||
if not str: print help
|
||||
else: print "ERROR",str
|
||||
sys.exit()
|
||||
|
||||
# parse args
|
||||
|
||||
args = sys.argv[1:]
|
||||
nargs = len(args)
|
||||
if nargs == 0: error()
|
||||
|
||||
machine = None
|
||||
extraflag = 0
|
||||
|
||||
iarg = 0
|
||||
while iarg < nargs:
|
||||
if args[iarg] == "-m":
|
||||
if iarg+2 > nargs: error()
|
||||
machine = args[iarg+1]
|
||||
iarg += 2
|
||||
elif args[iarg] == "-e":
|
||||
if iarg+2 > nargs: error()
|
||||
extraflag = 1
|
||||
suffix = args[iarg+1]
|
||||
iarg += 2
|
||||
else: error()
|
||||
|
||||
# set lib from working dir
|
||||
|
||||
cwd = os.getcwd()
|
||||
lib = os.path.basename(cwd)
|
||||
|
||||
# create Makefile.auto as copy of Makefile.machine
|
||||
# reset EXTRAMAKE if requested
|
||||
|
||||
if not os.path.exists("Makefile.%s" % machine):
|
||||
error("lib/%s/Makefile.%s does not exist" % (lib,machine))
|
||||
|
||||
lines = open("Makefile.%s" % machine,'r').readlines()
|
||||
fp = open("Makefile.auto",'w')
|
||||
|
||||
for line in lines:
|
||||
words = line.split()
|
||||
if len(words) == 3 and extraflag and \
|
||||
words[0] == "EXTRAMAKE" and words[1] == '=':
|
||||
line = line.replace(words[2],"Makefile.lammps.%s" % suffix)
|
||||
print >>fp,line,
|
||||
|
||||
fp.close()
|
||||
|
||||
# make the library via Makefile.auto
|
||||
|
||||
print "Building lib%s.a ..." % lib
|
||||
cmd = "make -f Makefile.auto clean; make -f Makefile.auto"
|
||||
txt = commands.getoutput(cmd)
|
||||
print txt
|
||||
|
||||
if os.path.exists("lib%s.a" % lib): print "Build was successful"
|
||||
else: error("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib))
|
||||
if not os.path.exists("Makefile.lammps"):
|
||||
print "lib/%s/Makefile.lammps was NOT created" % lib
|
||||
|
|
@ -0,0 +1 @@
|
|||
Install.py
|
||||
|
|
@ -1,82 +0,0 @@
|
|||
#!/usr/bin/env python
|
||||
|
||||
# install.py tool to do a generic build of a library
|
||||
# soft linked to by many of the lib/Install.py files
|
||||
# used to automate the steps described in the corresponding lib/README
|
||||
|
||||
import sys,commands,os
|
||||
|
||||
# help message
|
||||
|
||||
help = """
|
||||
Syntax: python Install.py -m machine -e suffix
|
||||
specify -m and optionally -e, order does not matter
|
||||
-m = peform a clean followed by "make -f Makefile.machine"
|
||||
machine = suffix of a lib/Makefile.* file
|
||||
-e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
|
||||
does not alter existing Makefile.machine
|
||||
"""
|
||||
|
||||
# print error message or help
|
||||
|
||||
def error(str=None):
|
||||
if not str: print help
|
||||
else: print "ERROR",str
|
||||
sys.exit()
|
||||
|
||||
# parse args
|
||||
|
||||
args = sys.argv[1:]
|
||||
nargs = len(args)
|
||||
if nargs == 0: error()
|
||||
|
||||
machine = None
|
||||
extraflag = 0
|
||||
|
||||
iarg = 0
|
||||
while iarg < nargs:
|
||||
if args[iarg] == "-m":
|
||||
if iarg+2 > nargs: error()
|
||||
machine = args[iarg+1]
|
||||
iarg += 2
|
||||
elif args[iarg] == "-e":
|
||||
if iarg+2 > nargs: error()
|
||||
extraflag = 1
|
||||
suffix = args[iarg+1]
|
||||
iarg += 2
|
||||
else: error()
|
||||
|
||||
# set lib from working dir
|
||||
|
||||
cwd = os.getcwd()
|
||||
lib = os.path.basename(cwd)
|
||||
|
||||
# create Makefile.auto as copy of Makefile.machine
|
||||
# reset EXTRAMAKE if requested
|
||||
|
||||
if not os.path.exists("Makefile.%s" % machine):
|
||||
error("lib/%s/Makefile.%s does not exist" % (lib,machine))
|
||||
|
||||
lines = open("Makefile.%s" % machine,'r').readlines()
|
||||
fp = open("Makefile.auto",'w')
|
||||
|
||||
for line in lines:
|
||||
words = line.split()
|
||||
if len(words) == 3 and extraflag and \
|
||||
words[0] == "EXTRAMAKE" and words[1] == '=':
|
||||
line = line.replace(words[2],"Makefile.lammps.%s" % suffix)
|
||||
print >>fp,line,
|
||||
|
||||
fp.close()
|
||||
|
||||
# make the library via Makefile.auto
|
||||
|
||||
print "Building lib%s.a ..." % lib
|
||||
cmd = "make -f Makefile.auto clean; make -f Makefile.auto"
|
||||
txt = commands.getoutput(cmd)
|
||||
print txt
|
||||
|
||||
if os.path.exists("lib%s.a" % lib): print "Build was successful"
|
||||
else: error("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib))
|
||||
if not os.path.exists("Makefile.lammps"):
|
||||
print "lib/%s/Makefile.lammps was NOT created" % lib
|
||||
|
|
@ -0,0 +1 @@
|
|||
Install.py
|
||||
|
|
@ -1,82 +0,0 @@
|
|||
#!/usr/bin/env python
|
||||
|
||||
# install.py tool to do a generic build of a library
|
||||
# soft linked to by many of the lib/Install.py files
|
||||
# used to automate the steps described in the corresponding lib/README
|
||||
|
||||
import sys,commands,os
|
||||
|
||||
# help message
|
||||
|
||||
help = """
|
||||
Syntax: python Install.py -m machine -e suffix
|
||||
specify -m and optionally -e, order does not matter
|
||||
-m = peform a clean followed by "make -f Makefile.machine"
|
||||
machine = suffix of a lib/Makefile.* file
|
||||
-e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
|
||||
does not alter existing Makefile.machine
|
||||
"""
|
||||
|
||||
# print error message or help
|
||||
|
||||
def error(str=None):
|
||||
if not str: print help
|
||||
else: print "ERROR",str
|
||||
sys.exit()
|
||||
|
||||
# parse args
|
||||
|
||||
args = sys.argv[1:]
|
||||
nargs = len(args)
|
||||
if nargs == 0: error()
|
||||
|
||||
machine = None
|
||||
extraflag = 0
|
||||
|
||||
iarg = 0
|
||||
while iarg < nargs:
|
||||
if args[iarg] == "-m":
|
||||
if iarg+2 > nargs: error()
|
||||
machine = args[iarg+1]
|
||||
iarg += 2
|
||||
elif args[iarg] == "-e":
|
||||
if iarg+2 > nargs: error()
|
||||
extraflag = 1
|
||||
suffix = args[iarg+1]
|
||||
iarg += 2
|
||||
else: error()
|
||||
|
||||
# set lib from working dir
|
||||
|
||||
cwd = os.getcwd()
|
||||
lib = os.path.basename(cwd)
|
||||
|
||||
# create Makefile.auto as copy of Makefile.machine
|
||||
# reset EXTRAMAKE if requested
|
||||
|
||||
if not os.path.exists("Makefile.%s" % machine):
|
||||
error("lib/%s/Makefile.%s does not exist" % (lib,machine))
|
||||
|
||||
lines = open("Makefile.%s" % machine,'r').readlines()
|
||||
fp = open("Makefile.auto",'w')
|
||||
|
||||
for line in lines:
|
||||
words = line.split()
|
||||
if len(words) == 3 and extraflag and \
|
||||
words[0] == "EXTRAMAKE" and words[1] == '=':
|
||||
line = line.replace(words[2],"Makefile.lammps.%s" % suffix)
|
||||
print >>fp,line,
|
||||
|
||||
fp.close()
|
||||
|
||||
# make the library via Makefile.auto
|
||||
|
||||
print "Building lib%s.a ..." % lib
|
||||
cmd = "make -f Makefile.auto clean; make -f Makefile.auto"
|
||||
txt = commands.getoutput(cmd)
|
||||
print txt
|
||||
|
||||
if os.path.exists("lib%s.a" % lib): print "Build was successful"
|
||||
else: error("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib))
|
||||
if not os.path.exists("Makefile.lammps"):
|
||||
print "lib/%s/Makefile.lammps was NOT created" % lib
|
||||
|
|
@ -0,0 +1 @@
|
|||
Install.py
|
||||
|
|
@ -1,82 +0,0 @@
|
|||
#!/usr/bin/env python
|
||||
|
||||
# install.py tool to do a generic build of a library
|
||||
# soft linked to by many of the lib/Install.py files
|
||||
# used to automate the steps described in the corresponding lib/README
|
||||
|
||||
import sys,commands,os
|
||||
|
||||
# help message
|
||||
|
||||
help = """
|
||||
Syntax: python Install.py -m machine -e suffix
|
||||
specify -m and optionally -e, order does not matter
|
||||
-m = peform a clean followed by "make -f Makefile.machine"
|
||||
machine = suffix of a lib/Makefile.* file
|
||||
-e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
|
||||
does not alter existing Makefile.machine
|
||||
"""
|
||||
|
||||
# print error message or help
|
||||
|
||||
def error(str=None):
|
||||
if not str: print help
|
||||
else: print "ERROR",str
|
||||
sys.exit()
|
||||
|
||||
# parse args
|
||||
|
||||
args = sys.argv[1:]
|
||||
nargs = len(args)
|
||||
if nargs == 0: error()
|
||||
|
||||
machine = None
|
||||
extraflag = 0
|
||||
|
||||
iarg = 0
|
||||
while iarg < nargs:
|
||||
if args[iarg] == "-m":
|
||||
if iarg+2 > nargs: error()
|
||||
machine = args[iarg+1]
|
||||
iarg += 2
|
||||
elif args[iarg] == "-e":
|
||||
if iarg+2 > nargs: error()
|
||||
extraflag = 1
|
||||
suffix = args[iarg+1]
|
||||
iarg += 2
|
||||
else: error()
|
||||
|
||||
# set lib from working dir
|
||||
|
||||
cwd = os.getcwd()
|
||||
lib = os.path.basename(cwd)
|
||||
|
||||
# create Makefile.auto as copy of Makefile.machine
|
||||
# reset EXTRAMAKE if requested
|
||||
|
||||
if not os.path.exists("Makefile.%s" % machine):
|
||||
error("lib/%s/Makefile.%s does not exist" % (lib,machine))
|
||||
|
||||
lines = open("Makefile.%s" % machine,'r').readlines()
|
||||
fp = open("Makefile.auto",'w')
|
||||
|
||||
for line in lines:
|
||||
words = line.split()
|
||||
if len(words) == 3 and extraflag and \
|
||||
words[0] == "EXTRAMAKE" and words[1] == '=':
|
||||
line = line.replace(words[2],"Makefile.lammps.%s" % suffix)
|
||||
print >>fp,line,
|
||||
|
||||
fp.close()
|
||||
|
||||
# make the library via Makefile.auto
|
||||
|
||||
print "Building lib%s.a ..." % lib
|
||||
cmd = "make -f Makefile.auto clean; make -f Makefile.auto"
|
||||
txt = commands.getoutput(cmd)
|
||||
print txt
|
||||
|
||||
if os.path.exists("lib%s.a" % lib): print "Build was successful"
|
||||
else: error("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib))
|
||||
if not os.path.exists("Makefile.lammps"):
|
||||
print "lib/%s/Makefile.lammps was NOT created" % lib
|
||||
|
|
@ -0,0 +1 @@
|
|||
Install.py
|
||||
|
|
@ -446,7 +446,7 @@ void FixMSST::initial_integrate(int vflag)
|
|||
{
|
||||
int i,k;
|
||||
double p_msst; // MSST driving pressure
|
||||
double vol,TS,TS_term,escale_term;
|
||||
double vol;
|
||||
|
||||
int nlocal = atom->nlocal;
|
||||
int *mask = atom->mask;
|
||||
|
|
@ -469,12 +469,16 @@ void FixMSST::initial_integrate(int vflag)
|
|||
// must convert energy to mv^2 units
|
||||
|
||||
if (dftb) {
|
||||
double TS_dftb = fix_external->compute_vector(0);
|
||||
TS = force->ftm2v*TS_dftb;
|
||||
const double TS_dftb = fix_external->compute_vector(0);
|
||||
const double TS = force->ftm2v*TS_dftb;
|
||||
// update S_elec terms and compute TS_dot via finite differences
|
||||
S_elec_2 = S_elec_1;
|
||||
S_elec_1 = S_elec;
|
||||
const double Temp = temperature->compute_scalar();
|
||||
S_elec = TS/Temp;
|
||||
TS_dot = Temp*(3.0*S_elec-4.0*S_elec_1+S_elec_2)/(2.0*update->dt);
|
||||
TS_int += (update->dt*TS_dot);
|
||||
if (update->ntimestep == 1) T0S0 = TS;
|
||||
} else {
|
||||
TS = 0.0;
|
||||
T0S0 = 0.0;
|
||||
}
|
||||
|
||||
// compute new pressure and volume
|
||||
|
|
@ -484,16 +488,6 @@ void FixMSST::initial_integrate(int vflag)
|
|||
couple();
|
||||
vol = compute_vol();
|
||||
|
||||
// update S_elec terms and compute TS_dot via finite differences
|
||||
|
||||
S_elec_2 = S_elec_1;
|
||||
S_elec_1 = S_elec;
|
||||
double Temp = temperature->compute_scalar();
|
||||
S_elec = TS/Temp;
|
||||
TS_dot = Temp*(3.0*S_elec-4.0*S_elec_1+S_elec_2)/(2.0*update->dt);
|
||||
TS_int += (update->dt*TS_dot);
|
||||
//TS_int += (update->dt*TS_dot)/total_mass;
|
||||
|
||||
// compute etot + extra terms for conserved quantity
|
||||
|
||||
double e_scale = compute_etotal() + compute_scalar();
|
||||
|
|
@ -530,9 +524,9 @@ void FixMSST::initial_integrate(int vflag)
|
|||
for (i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
for ( k = 0; k < 3; k++ ) {
|
||||
double C = f[i][k] * force->ftm2v / mass[type[i]];
|
||||
TS_term = TS_dot/(mass[type[i]]*velocity_sum);
|
||||
escale_term = force->ftm2v*beta*(e0-e_scale) /
|
||||
const double C = f[i][k] * force->ftm2v / mass[type[i]];
|
||||
const double TS_term = TS_dot/(mass[type[i]]*velocity_sum);
|
||||
const double escale_term = force->ftm2v*beta*(e0-e_scale) /
|
||||
(mass[type[i]]*velocity_sum);
|
||||
double D = mu * omega[sd] * omega[sd] /
|
||||
(velocity_sum * mass[type[i]] * vol );
|
||||
|
|
@ -540,7 +534,7 @@ void FixMSST::initial_integrate(int vflag)
|
|||
old_velocity[i][k] = v[i][k];
|
||||
if ( k == direction ) D -= 2.0 * omega[sd] / vol;
|
||||
if ( fabs(dthalf * D) > 1.0e-06 ) {
|
||||
double expd = exp(D * dthalf);
|
||||
const double expd = exp(D * dthalf);
|
||||
v[i][k] = expd * ( C + D * v[i][k] - C / expd ) / D;
|
||||
} else {
|
||||
v[i][k] = v[i][k] + ( C + D * v[i][k] ) * dthalf +
|
||||
|
|
@ -553,15 +547,15 @@ void FixMSST::initial_integrate(int vflag)
|
|||
for (i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
for ( k = 0; k < 3; k++ ) {
|
||||
double C = f[i][k] * force->ftm2v / mass[type[i]];
|
||||
const double C = f[i][k] * force->ftm2v / mass[type[i]];
|
||||
double D = mu * omega[sd] * omega[sd] /
|
||||
(velocity_sum * mass[type[i]] * vol );
|
||||
old_velocity[i][k] = v[i][k];
|
||||
if ( k == direction ) {
|
||||
D = D - 2.0 * omega[sd] / vol;
|
||||
D -= 2.0 * omega[sd] / vol;
|
||||
}
|
||||
if ( fabs(dthalf * D) > 1.0e-06 ) {
|
||||
double expd = exp(D * dthalf);
|
||||
const double expd = exp(D * dthalf);
|
||||
v[i][k] = expd * ( C + D * v[i][k] - C / expd ) / D;
|
||||
} else {
|
||||
v[i][k] = v[i][k] + ( C + D * v[i][k] ) * dthalf +
|
||||
|
|
@ -590,16 +584,16 @@ void FixMSST::initial_integrate(int vflag)
|
|||
for (i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
for ( k = 0; k < 3; k++ ) {
|
||||
double C = f[i][k] * force->ftm2v / mass[type[i]];
|
||||
TS_term = TS_dot/(mass[type[i]]*velocity_sum);
|
||||
escale_term = force->ftm2v*beta*(e0-e_scale) /
|
||||
const double C = f[i][k] * force->ftm2v / mass[type[i]];
|
||||
const double TS_term = TS_dot/(mass[type[i]]*velocity_sum);
|
||||
const double escale_term = force->ftm2v*beta*(e0-e_scale) /
|
||||
(mass[type[i]]*velocity_sum);
|
||||
double D = mu * omega[sd] * omega[sd] /
|
||||
(velocity_sum * mass[type[i]] * vol );
|
||||
D += escale_term - TS_term;
|
||||
if ( k == direction ) D -= 2.0 * omega[sd] / vol;
|
||||
if ( fabs(dthalf * D) > 1.0e-06 ) {
|
||||
double expd = exp(D * dthalf);
|
||||
const double expd = exp(D * dthalf);
|
||||
v[i][k] = expd * ( C + D * v[i][k] - C / expd ) / D;
|
||||
} else {
|
||||
v[i][k] = v[i][k] + ( C + D * v[i][k] ) * dthalf +
|
||||
|
|
@ -612,14 +606,14 @@ void FixMSST::initial_integrate(int vflag)
|
|||
for (i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
for ( k = 0; k < 3; k++ ) {
|
||||
double C = f[i][k] * force->ftm2v / mass[type[i]];
|
||||
const double C = f[i][k] * force->ftm2v / mass[type[i]];
|
||||
double D = mu * omega[sd] * omega[sd] /
|
||||
(velocity_sum * mass[type[i]] * vol );
|
||||
if ( k == direction ) {
|
||||
D = D - 2.0 * omega[sd] / vol;
|
||||
D -= 2.0 * omega[sd] / vol;
|
||||
}
|
||||
if ( fabs(dthalf * D) > 1.0e-06 ) {
|
||||
double expd = exp(D * dthalf);
|
||||
const double expd = exp(D * dthalf);
|
||||
v[i][k] = expd * ( C + D * v[i][k] - C / expd ) / D;
|
||||
} else {
|
||||
v[i][k] = v[i][k] + ( C + D * v[i][k] ) * dthalf +
|
||||
|
|
@ -669,7 +663,6 @@ void FixMSST::final_integrate()
|
|||
{
|
||||
int i;
|
||||
double p_msst; // MSST driving pressure
|
||||
double TS_term,escale_term;
|
||||
|
||||
// v update only for atoms in MSST group
|
||||
|
||||
|
|
@ -687,22 +680,38 @@ void FixMSST::final_integrate()
|
|||
|
||||
double e_scale = compute_etotal() + compute_scalar();
|
||||
|
||||
// for DFTB, extract TS_dftb from fix external
|
||||
// must convert energy to mv^2 units
|
||||
|
||||
if (dftb) {
|
||||
const double TS_dftb = fix_external->compute_vector(0);
|
||||
const double TS = force->ftm2v*TS_dftb;
|
||||
S_elec_2 = S_elec_1;
|
||||
S_elec_1 = S_elec;
|
||||
const double Temp = temperature->compute_scalar();
|
||||
// update S_elec terms and compute TS_dot via finite differences
|
||||
S_elec = TS/Temp;
|
||||
TS_dot = Temp*(3.0*S_elec-4.0*S_elec_1+S_elec_2)/(2.0*update->dt);
|
||||
TS_int += (update->dt*TS_dot);
|
||||
if (update->ntimestep == 1) T0S0 = TS;
|
||||
}
|
||||
|
||||
// propagate particle velocities 1/2 step
|
||||
|
||||
if (dftb) {
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
for ( int k = 0; k < 3; k++ ) {
|
||||
double C = f[i][k] * force->ftm2v / mass[type[i]];
|
||||
TS_term = TS_dot/(mass[type[i]]*velocity_sum);
|
||||
escale_term = force->ftm2v*beta*(e0-e_scale) /
|
||||
const double C = f[i][k] * force->ftm2v / mass[type[i]];
|
||||
const double TS_term = TS_dot/(mass[type[i]]*velocity_sum);
|
||||
const double escale_term = force->ftm2v*beta*(e0-e_scale) /
|
||||
(mass[type[i]]*velocity_sum);
|
||||
double D = mu * omega[sd] * omega[sd] /
|
||||
(velocity_sum * mass[type[i]] * vol );
|
||||
D += escale_term - TS_term;
|
||||
if ( k == direction ) D -= 2.0 * omega[sd] / vol;
|
||||
if ( fabs(dthalf * D) > 1.0e-06 ) {
|
||||
double expd = exp(D * dthalf);
|
||||
const double expd = exp(D * dthalf);
|
||||
v[i][k] = expd * ( C + D * v[i][k] - C / expd ) / D;
|
||||
} else {
|
||||
v[i][k] = v[i][k] + ( C + D * v[i][k] ) * dthalf +
|
||||
|
|
@ -715,14 +724,14 @@ void FixMSST::final_integrate()
|
|||
for (i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
for ( int k = 0; k < 3; k++ ) {
|
||||
double C = f[i][k] * force->ftm2v / mass[type[i]];
|
||||
const double C = f[i][k] * force->ftm2v / mass[type[i]];
|
||||
double D = mu * omega[sd] * omega[sd] /
|
||||
(velocity_sum * mass[type[i]] * vol );
|
||||
if ( k == direction ) {
|
||||
D = D - 2.0 * omega[sd] / vol;
|
||||
D -= 2.0 * omega[sd] / vol;
|
||||
}
|
||||
if ( fabs(dthalf * D) > 1.0e-06 ) {
|
||||
double expd = exp(D * dthalf);
|
||||
const double expd = exp(D * dthalf);
|
||||
v[i][k] = expd * ( C + D * v[i][k] - C / expd ) / D;
|
||||
} else {
|
||||
v[i][k] = v[i][k] + ( C + D * v[i][k] ) * dthalf +
|
||||
|
|
@ -748,7 +757,7 @@ void FixMSST::final_integrate()
|
|||
( v0 - vol )/( v0 * v0 );
|
||||
double A = total_mass * ( p_current[sd] - p0 - p_msst ) /
|
||||
( qmass * nktv2p * mvv2e );
|
||||
double B = total_mass * mu / ( qmass * vol );
|
||||
const double B = total_mass * mu / ( qmass * vol );
|
||||
|
||||
// prevent blow-up of the volume
|
||||
|
||||
|
|
@ -950,7 +959,9 @@ double FixMSST::compute_scalar()
|
|||
|
||||
// subtract off precomputed TS_int integral value
|
||||
|
||||
energy -= TS_int;
|
||||
if (dftb) { // TS_int == 0 for non DFTB calculations
|
||||
energy -= TS_int;
|
||||
}
|
||||
|
||||
return energy;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -936,7 +936,7 @@ int Balance::shift()
|
|||
// stop at this point in bstr if imbalance factor < threshold
|
||||
// this is a true 3d test of particle count per processor
|
||||
|
||||
double imbfactor = imbalance_splits(max);
|
||||
double imbfactor = imbalance_splits();
|
||||
if (imbfactor <= stopthresh) break;
|
||||
}
|
||||
|
||||
|
|
@ -1047,11 +1047,10 @@ int Balance::adjust(int n, double *split)
|
|||
calculate imbalance based on processor splits in 3 dims
|
||||
atoms must be in lamda coords (0-1) before called
|
||||
map particles to 3d grid of procs
|
||||
return maxcost = max load per proc
|
||||
return imbalance factor = max load per proc / ave load per proc
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double Balance::imbalance_splits(int &maxcost)
|
||||
double Balance::imbalance_splits()
|
||||
{
|
||||
double *xsplit = comm->xsplit;
|
||||
double *ysplit = comm->ysplit;
|
||||
|
|
@ -1088,7 +1087,7 @@ double Balance::imbalance_splits(int &maxcost)
|
|||
|
||||
MPI_Allreduce(proccost,allproccost,nprocs,MPI_DOUBLE,MPI_SUM,world);
|
||||
|
||||
maxcost = 0.0;
|
||||
double maxcost = 0.0;
|
||||
double totalcost = 0.0;
|
||||
for (int i = 0; i < nprocs; i++) {
|
||||
maxcost = MAX(maxcost,allproccost[i]);
|
||||
|
|
|
|||
|
|
@ -81,7 +81,7 @@ class Balance : protected Pointers {
|
|||
FILE *fp; // balance output file
|
||||
int firststep;
|
||||
|
||||
double imbalance_splits(int &);
|
||||
double imbalance_splits();
|
||||
void shift_setup_static(char *);
|
||||
void tally(int, int, double *);
|
||||
int adjust(int, double *);
|
||||
|
|
|
|||
18
src/rcb.cpp
18
src/rcb.cpp
|
|
@ -288,7 +288,7 @@ void RCB::compute(int dimension, int n, double **x, double *wt,
|
|||
// use old value on 1st iteration if old cut dimension is the same
|
||||
// on 2nd option: could push valuehalf towards geometric center
|
||||
// with "1.0-factor" to force overshoot
|
||||
|
||||
|
||||
if (first_iteration && reuse && dim == tree[procmid].dim) {
|
||||
counters[5]++;
|
||||
valuehalf = tree[procmid].cut;
|
||||
|
|
@ -310,7 +310,7 @@ void RCB::compute(int dimension, int n, double **x, double *wt,
|
|||
medme.wtlo = medme.wthi = 0.0;
|
||||
medme.countlo = medme.counthi = 0;
|
||||
medme.proclo = medme.prochi = me;
|
||||
|
||||
|
||||
// mark all active dots on one side or other of bisector
|
||||
// also set all fields in median data struct
|
||||
// save indices of closest dots on either side
|
||||
|
|
@ -391,11 +391,11 @@ void RCB::compute(int dimension, int n, double **x, double *wt,
|
|||
|
||||
wtlo += med.wthi;
|
||||
if (targetlo-wtlo <= tolerance) break; // close enough
|
||||
|
||||
|
||||
valuemin = med.valuehi; // iterate again
|
||||
markactive = 1;
|
||||
}
|
||||
|
||||
|
||||
else if (wthi + med.totalhi < targethi) { // upper half TOO SMALL
|
||||
|
||||
wthi += med.totalhi;
|
||||
|
|
@ -431,7 +431,7 @@ void RCB::compute(int dimension, int n, double **x, double *wt,
|
|||
}
|
||||
if (breakflag) break; // done if moved enough
|
||||
}
|
||||
|
||||
|
||||
wthi += med.wtlo;
|
||||
if (targethi-wthi <= tolerance) break; // close enough
|
||||
|
||||
|
|
@ -455,13 +455,13 @@ void RCB::compute(int dimension, int n, double **x, double *wt,
|
|||
// cut produces 2 sub-boxes with reduced size in dim
|
||||
// compare smaller of the 2 sizes to previous dims
|
||||
// keep dim that has the largest smaller
|
||||
|
||||
|
||||
smaller = MIN(valuehalf-lo[dim],hi[dim]-valuehalf);
|
||||
if (smaller > largest) {
|
||||
largest = smaller;
|
||||
dim_select = dim;
|
||||
valuehalf_select = valuehalf;
|
||||
memcpy(dotmark_select,dotmark,ndot*sizeof(int));
|
||||
if (ndot > 0) memcpy(dotmark_select,dotmark,ndot*sizeof(int));
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -469,11 +469,11 @@ void RCB::compute(int dimension, int n, double **x, double *wt,
|
|||
|
||||
dim = dim_select;
|
||||
valuehalf = valuehalf_select;
|
||||
memcpy(dotmark,dotmark_select,ndot*sizeof(int));
|
||||
if (ndot > 0) memcpy(dotmark,dotmark_select,ndot*sizeof(int));
|
||||
|
||||
// found median
|
||||
// store cut info only if I am procmid
|
||||
|
||||
|
||||
if (me == procmid) {
|
||||
cut = valuehalf;
|
||||
cutdim = dim;
|
||||
|
|
|
|||
Loading…
Reference in New Issue