download only the plumed-src package and include further tweaks to be compatible with plumed 2.5b (badfdd74) · Commits · 郑智淋 / lammps

examples/USER/plumed/log.24Oct18.peptide-plumed.g++.4

+23 −23

Original line number	Diff line number	Diff line
		@@ -15,7 +15,7 @@ kspace_style pppm 0.0001

		read_data data.peptide
		orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
		1 by 1 by 2 MPI processor grid
		1 by 2 by 2 MPI processor grid
		reading atoms ...
		2004 atoms
		reading velocities ...
		@@ -85,7 +85,7 @@ PPPM initialization ...
		estimated absolute RMS force accuracy = 0.0228209
		estimated relative force accuracy = 6.87243e-05
		using double precision FFTs
		3d grid and FFT values/proc = 6776 1800
		3d grid and FFT values/proc = 4312 960
		Neighbor list info ...
		update every 1 steps, delay 5 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		@@ -107,7 +107,7 @@ SHAKE stats (type/ave/delta) on step 0
		14 0.96 0
		18 0.957206 4.37979e-05
		31 104.519 0.00396029
		Per MPI rank memory allocation (min/avg/max) = 16.81 \| 16.82 \| 16.83 Mbytes
		Per MPI rank memory allocation (min/avg/max) = 15.65 \| 15.86 \| 16.05 Mbytes
		Step Temp TotEng PotEng KinEng E_pair E_bond f_2
		0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 0
		10 276.9783 -5234.3057 -6348.6171 1114.3114 -6421.6171 17.024361 0.47785504
		@@ -118,7 +118,7 @@ Step Temp TotEng PotEng KinEng E_pair E_bond f_2
		60 273.01449 -5217.7381 -6316.1026 1098.3646 -6406.4709 21.800931 0.92327815
		70 274.67549 -5221.0246 -6326.0716 1105.047 -6409.7721 19.41235 0.0016975896
		80 273.74824 -5224.7613 -6326.0778 1101.3165 -6418.5055 19.206793 0.48550348
		90 284.32594 -5229.195 -6373.0667 1143.8717 -6461.3467 21.124789 0.5468014
		90 284.32594 -5229.195 -6373.0667 1143.8717 -6461.3466 21.124789 0.5468014
		SHAKE stats (type/ave/delta) on step 100
		4 1.111 2.06868e-06
		6 0.996999 2.09521e-06
		@@ -128,31 +128,31 @@ SHAKE stats (type/ave/delta) on step 100
		14 0.959999 0
		18 0.9572 9.14098e-06
		31 104.52 0.000760401
		100 270.40648 -5234.9604 -6322.8327 1087.8723 -6417.73 19.666404 0.0094784372
		100 270.40648 -5234.9604 -6322.8327 1087.8723 -6417.73 19.666404 0.009478437
		101 270.99811 -5235.8295 -6326.082 1090.2525 -6418.8974 17.285816 0.086681332
		Loop time of 1.23137 on 2 procs for 101 steps with 2004 atoms
		Loop time of 1.16767 on 4 procs for 101 steps with 2004 atoms

		Performance: 14.173 ns/day, 1.693 hours/ns, 82.022 timesteps/s
		99.5% CPU use with 2 MPI tasks x 1 OpenMP threads
		Performance: 14.947 ns/day, 1.606 hours/ns, 86.497 timesteps/s
		97.8% CPU use with 4 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 0.97985 \| 0.98197 \| 0.98409 \| 0.2 \| 79.75
		Bond \| 0.0033333 \| 0.0035326 \| 0.003732 \| 0.3 \| 0.29
		Kspace \| 0.096567 \| 0.098457 \| 0.10035 \| 0.6 \| 8.00
		Neigh \| 0.088877 \| 0.088888 \| 0.088898 \| 0.0 \| 7.22
		Comm \| 0.018255 \| 0.018347 \| 0.01844 \| 0.1 \| 1.49
		Output \| 0.00024843 \| 0.00031161 \| 0.00037479 \| 0.0 \| 0.03
		Modify \| 0.037596 \| 0.037645 \| 0.037695 \| 0.0 \| 3.06
		Other \| \| 0.00222 \| \| \| 0.18

		Nlocal: 1002 ave 1010 max 994 min
		Histogram: 1 0 0 0 0 0 0 0 0 1
		Nghost: 8639.5 ave 8651 max 8628 min
		Histogram: 1 0 0 0 0 0 0 0 0 1
		Neighs: 353980 ave 355907 max 352054 min
		Histogram: 1 0 0 0 0 0 0 0 0 1
		Pair \| 0.84633 \| 0.86651 \| 0.88617 \| 1.6 \| 74.21
		Bond \| 0.0010614 \| 0.0027132 \| 0.004288 \| 3.0 \| 0.23
		Kspace \| 0.095008 \| 0.1162 \| 0.13491 \| 4.3 \| 9.95
		Neigh \| 0.07834 \| 0.078424 \| 0.078516 \| 0.0 \| 6.72
		Comm \| 0.03314 \| 0.033299 \| 0.033426 \| 0.1 \| 2.85
		Output \| 0.00036979 \| 0.00076199 \| 0.0019338 \| 0.0 \| 0.07
		Modify \| 0.063471 \| 0.064011 \| 0.065312 \| 0.3 \| 5.48
		Other \| \| 0.005751 \| \| \| 0.49

		Nlocal: 501 ave 512 max 492 min
		Histogram: 1 0 0 1 0 1 0 0 0 1
		Nghost: 6570.25 ave 6604 max 6529 min
		Histogram: 1 0 0 1 0 0 0 0 1 1
		Neighs: 176990 ave 181122 max 173551 min
		Histogram: 1 1 0 0 0 0 1 0 0 1

		Total # of neighbors = 707961
		Ave neighs/atom = 353.274

lib/plumed/Install.py

+23 −10

Original line number	Diff line number	Diff line
		@@ -35,10 +35,16 @@ version = "2.4.3"

		# known checksums for different PLUMED versions. used to validate the download.
		checksums = { \
		'2.4.2' : '0f66f24b4c763ae8b2f39574113e9935', \
		'2.4.3' : 'dc38de0ffd59d13950d8f1ef1ce05574', \
		'2.4.2' : '88188743a6e03ef076e5377d03ebb0e7', \
		'2.4.3' : 'b1be7c48971627febc11c61b70767fc5', \
		'2.5b' : 'e341bdef469be1da058b8a0b97a3db22', \
		}

		#checksums = { \
		# '2.4.2' : '0f66f24b4c763ae8b2f39574113e9935', \
		# '2.4.3' : 'dc38de0ffd59d13950d8f1ef1ce05574', \
		# }

		# print error message or help
		def error(str=None):
		if not str: print(help)
		@@ -146,8 +152,10 @@ if (not buildflag and not pathflag):
		# download and unpack plumed2 tarball

		if buildflag:
		url = "https://github.com/plumed/plumed2/archive/v%s.tar.gz" % version
		filename = "v%s.tar.gz" %version
		url = "https://github.com/plumed/plumed2/releases/download/v%s/plumed-src-%s.tgz" % (version,version)
		filename = "plumed-src-%s.tar.gz" %version
		#url = "https://github.com/plumed/plumed2/archive/v%s.tar.gz" % version
		#filename = "v%s.tar.gz" %version
		print("Downloading plumed ...")
		geturl(url,filename)

		@@ -156,22 +164,26 @@ if buildflag:
		if not checkmd5sum(checksums[version],filename):
		error("Checksum for plumed2 library does not match")

		print("Unpacking plumed2 tarball ...")
		if os.path.exists("%s/plumed2-%s" % (homepath,version)):
		cmd = 'rm -rf "%s/plumed2-%s"' % (homepath,version)
		print("Unpacking plumed2 source tarball ...")
		if os.path.exists("%s/plumed-%s" % (homepath,version)):
		cmd = 'rm -rf "%s/plumed-%s"' % (homepath,version)
		subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
		#if os.path.exists("%s/plumed2-%s" % (homepath,version)):
		# cmd = 'rm -rf "%s/plumed2-%s"' % (homepath,version)
		# subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
		if os.path.exists("%s/plumed2" % (homepath)):
		cmd = 'rm -rf "%s/plumed2"' % (homepath)
		subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
		cmd = 'cd "%s"; tar -xzvf v%s.tar.gz' % (homepath,version)
		cmd = 'cd "%s"; tar -xzvf %s' % (homepath,filename)
		subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
		os.remove("%s/v%s.tar.gz" % (homepath,version))
		os.remove("%s/%s" % (homepath,filename))

		# build plumed

		if buildflag:
		print("Building plumed ...")
		cmd = 'cd %s/plumed2-%s; ./configure --prefix=%s/plumed2 ; make ; make install' % (homepath,version,homepath)
		cmd = 'cd %s/plumed-%s; ./configure --prefix=%s/plumed2 --enable-static-patch ; make ; make install' % (homepath,version,homepath)
		#cmd = 'cd %s/plumed2-%s; ./configure --prefix=%s/plumed2 --enable-static-patch ; make ; make install' % (homepath,version,homepath)
		txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
		print(txt.decode('UTF-8'))
		#
		@@ -190,4 +202,5 @@ if linkflag:
		if os.path.isfile("Makefile.lammps.static"):
		print("Creating Makefile.lammps")
		cmd = 'cat liblink/plumed/src/lib/Plumed.inc.static Makefile.lammps.static > Makefile.lammps'
		subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)

src/USER-PLUMED/fix_plumed.cpp

+2 −18

Original line number	Diff line number	Diff line
		@@ -34,25 +34,9 @@
		#include "pair.h"

		/*
		Do not link plumed directly but rather do it at runtime
		Use statically linked C++ interface to plumed
		*/
		#define __PLUMED_WRAPPER_LINK_RUNTIME 1

		/*
		Make sure the inline C++ interface is not included here.
		Should not be necessary, but it doesn't hurt.
		*/
		#define __PLUMED_WRAPPER_CXX 0

		/*
		Tell Plumed.h to emit the whole implementation
		*/
		#define __PLUMED_WRAPPER_IMPLEMENTATION 1

		/*
		Emit fortran wrappers
		*/
		#define __PLUMED_WRAPPER_FORTRAN 1
		#define __PLUMED_WRAPPER_CXX 1

		#include "plumed/wrapper/Plumed.h"

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