Loading .github/CODEOWNERS +1 −0 Original line number Diff line number Diff line Loading @@ -16,6 +16,7 @@ src/COMPRESS/* @akohlmey src/GPU/* @ndtrung81 src/KOKKOS/* @stanmoore1 src/KIM/* @ellio167 src/LATTE/* @cnegre src/USER-CGDNA/* @ohenrich src/USER-CGSDK/* @akohlmey src/USER-COLVARS/* @giacomofiorin Loading examples/latte/in.latte.water.ch4.consecutive.md→examples/latte/in.latte.multiple +0 −0 File moved. View file examples/latte/latte.in +1 −1 Original line number Diff line number Diff line Loading @@ -9,7 +9,7 @@ LATTE INPUT FILE #General controls CONTROL{ xControl= 1 XCONTROL= 1 BASISTYPE= NONORTHO PARAMPATH= "./TBparam" KBT= 0.0 Loading examples/latte/log.21Jun18.latte.multiple.g++.1 0 → 100644 +171 −0 Original line number Diff line number Diff line LAMMPS (22 Jun 2018) units metal atom_style full atom_modify sort 0 0.0 # turn off sorting of the coordinates read_data data.water orthogonal box = (0 0 0) to (6.267 6.267 6.267) 1 by 1 by 1 MPI processor grid reading atoms ... 24 atoms 0 = max # of 1-2 neighbors 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors # initialize system velocity all create 0.0 87287 loop geom pair_style zero 1.0 pair_coeff * * neighbor 1.0 bin neigh_modify every 1 delay 0 check yes timestep 0.00025 fix 1 all nve fix 2 all latte NULL fix_modify 2 energy yes thermo_style custom step temp pe etotal press # dynamics thermo 10 run 10 Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2 ghost atom cutoff = 2 binsize = 1, bins = 7 7 7 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair zero, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 5.629 | 5.629 | 5.629 Mbytes Step Temp PotEng TotEng Press 0 0 -104.95596 -104.95596 48235.442 10 336.53107 -105.96027 -104.95977 97996.851 Loop time of 0.912921 on 1 procs for 10 steps with 24 atoms Performance: 0.237 ns/day, 101.436 hours/ns, 10.954 timesteps/s 6614.5% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.3392e-05 | 4.3392e-05 | 4.3392e-05 | 0.0 | 0.00 Bond | 3.8862e-05 | 3.8862e-05 | 3.8862e-05 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00036955 | 0.00036955 | 0.00036955 | 0.0 | 0.04 Output | 9.799e-05 | 9.799e-05 | 9.799e-05 | 0.0 | 0.01 Modify | 0.91199 | 0.91199 | 0.91199 | 0.0 | 99.90 Other | | 0.0003812 | | | 0.04 Nlocal: 24 ave 24 max 24 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 71 ave 71 max 71 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37 ave 37 max 37 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37 Ave neighs/atom = 1.54167 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 # Clear up previus calculation clear # simple CH4 molecule with LATTE units metal atom_style full atom_modify sort 0 0.0 # turn off sorting of the coordinates read_data data.ch4 triclinic box = (0 0 0) to (19.523 12.758 11.692) with tilt (0 0 0) 1 by 1 by 1 MPI processor grid reading atoms ... 5 atoms 0 = max # of 1-2 neighbors 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors # initialize system velocity all create 0.0 87287 loop geom pair_style zero 1.0 pair_coeff * * neighbor 1.0 bin neigh_modify every 1 delay 0 check yes timestep 0.00025 fix 1 all nve fix 2 all latte NULL fix_modify 2 energy yes thermo_style custom step temp pe etotal press # dynamics thermo 10 run 10 Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2 ghost atom cutoff = 2 binsize = 1, bins = 20 13 12 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair zero, perpetual attributes: half, newton on pair build: half/bin/newton/tri stencil: half/bin/3d/newton/tri bin: standard Per MPI rank memory allocation (min/avg/max) = 5.651 | 5.651 | 5.651 Mbytes Step Temp PotEng TotEng Press 0 0 -23.980353 -23.980353 348.02716 10 19.123149 -23.990297 -23.98041 18.774332 Loop time of 0.0415399 on 1 procs for 10 steps with 5 atoms Performance: 5.200 ns/day, 4.616 hours/ns, 240.732 timesteps/s 6674.9% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.722e-06 | 5.722e-06 | 5.722e-06 | 0.0 | 0.01 Bond | 7.6294e-06 | 7.6294e-06 | 7.6294e-06 | 0.0 | 0.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 1.8358e-05 | 1.8358e-05 | 1.8358e-05 | 0.0 | 0.04 Output | 2.0981e-05 | 2.0981e-05 | 2.0981e-05 | 0.0 | 0.05 Modify | 0.041394 | 0.041394 | 0.041394 | 0.0 | 99.65 Other | | 9.322e-05 | | | 0.22 Nlocal: 5 ave 5 max 5 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7 ave 7 max 7 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 10 ave 10 max 10 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 10 Ave neighs/atom = 2 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 Total wall time: 0:00:01 lib/latte/Install.py +27 −4 Original line number Diff line number Diff line Loading @@ -4,7 +4,7 @@ # used to automate the steps described in the README file in this dir from __future__ import print_function import sys,os,re,subprocess import sys,os,re,subprocess,hashlib # help message Loading @@ -24,7 +24,7 @@ specify one or more options, order does not matter -b = download and build the LATTE library -p = specify folder of existing LATTE installation -m = copy Makefile.lammps.suffix to Makefile.lammps -v = set version of LATTE library to download and set up (default = 1.1.1) -v = set version of LATTE library to download and set up (default = 1.2.1) Example: Loading @@ -36,6 +36,13 @@ make lib-latte args="-p $HOME/latte" # use existing LATTE installation version = '1.2.1' # known checksums for different LATTE versions. used to validate the download. checksums = { \ '1.1.0' : '533635721ee222d0ed2925a18fb5b294', \ '1.2.0' : '68bf0db879da5e068a71281020239ae7', \ '1.2.1' : 'bed76e7e76c545c36dd848a8f1fd35eb' \ } # print error message or help def error(str=None): Loading Loading @@ -91,6 +98,17 @@ def geturl(url,fname): error("Failed to download source code with 'curl' or 'wget'") return def checkmd5sum(md5sum,fname): with open(fname,'rb') as fh: m = hashlib.md5() while True: data = fh.read(81920) if not data: break m.update(data) fh.close() return m.hexdigest() == md5sum # parse args args = sys.argv[1:] Loading Loading @@ -144,7 +162,12 @@ if buildflag: print("Downloading LATTE ...") geturl(url,"LATTE.tar.gz") print("Unpacking LATTE zipfile ...") # verify downloaded archive integrity via md5 checksum, if known. if version in checksums: if not checkmd5sum(checksums[version],'LATTE.tar.gz'): error("Checksum for LATTE library does not match") print("Unpacking LATTE ...") if os.path.exists(lattedir): cmd = 'rm -rf "%s"' % lattedir subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) Loading Loading
.github/CODEOWNERS +1 −0 Original line number Diff line number Diff line Loading @@ -16,6 +16,7 @@ src/COMPRESS/* @akohlmey src/GPU/* @ndtrung81 src/KOKKOS/* @stanmoore1 src/KIM/* @ellio167 src/LATTE/* @cnegre src/USER-CGDNA/* @ohenrich src/USER-CGSDK/* @akohlmey src/USER-COLVARS/* @giacomofiorin Loading
examples/latte/in.latte.water.ch4.consecutive.md→examples/latte/in.latte.multiple +0 −0 File moved. View file
examples/latte/latte.in +1 −1 Original line number Diff line number Diff line Loading @@ -9,7 +9,7 @@ LATTE INPUT FILE #General controls CONTROL{ xControl= 1 XCONTROL= 1 BASISTYPE= NONORTHO PARAMPATH= "./TBparam" KBT= 0.0 Loading
examples/latte/log.21Jun18.latte.multiple.g++.1 0 → 100644 +171 −0 Original line number Diff line number Diff line LAMMPS (22 Jun 2018) units metal atom_style full atom_modify sort 0 0.0 # turn off sorting of the coordinates read_data data.water orthogonal box = (0 0 0) to (6.267 6.267 6.267) 1 by 1 by 1 MPI processor grid reading atoms ... 24 atoms 0 = max # of 1-2 neighbors 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors # initialize system velocity all create 0.0 87287 loop geom pair_style zero 1.0 pair_coeff * * neighbor 1.0 bin neigh_modify every 1 delay 0 check yes timestep 0.00025 fix 1 all nve fix 2 all latte NULL fix_modify 2 energy yes thermo_style custom step temp pe etotal press # dynamics thermo 10 run 10 Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2 ghost atom cutoff = 2 binsize = 1, bins = 7 7 7 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair zero, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 5.629 | 5.629 | 5.629 Mbytes Step Temp PotEng TotEng Press 0 0 -104.95596 -104.95596 48235.442 10 336.53107 -105.96027 -104.95977 97996.851 Loop time of 0.912921 on 1 procs for 10 steps with 24 atoms Performance: 0.237 ns/day, 101.436 hours/ns, 10.954 timesteps/s 6614.5% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.3392e-05 | 4.3392e-05 | 4.3392e-05 | 0.0 | 0.00 Bond | 3.8862e-05 | 3.8862e-05 | 3.8862e-05 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00036955 | 0.00036955 | 0.00036955 | 0.0 | 0.04 Output | 9.799e-05 | 9.799e-05 | 9.799e-05 | 0.0 | 0.01 Modify | 0.91199 | 0.91199 | 0.91199 | 0.0 | 99.90 Other | | 0.0003812 | | | 0.04 Nlocal: 24 ave 24 max 24 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 71 ave 71 max 71 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37 ave 37 max 37 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37 Ave neighs/atom = 1.54167 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 # Clear up previus calculation clear # simple CH4 molecule with LATTE units metal atom_style full atom_modify sort 0 0.0 # turn off sorting of the coordinates read_data data.ch4 triclinic box = (0 0 0) to (19.523 12.758 11.692) with tilt (0 0 0) 1 by 1 by 1 MPI processor grid reading atoms ... 5 atoms 0 = max # of 1-2 neighbors 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors # initialize system velocity all create 0.0 87287 loop geom pair_style zero 1.0 pair_coeff * * neighbor 1.0 bin neigh_modify every 1 delay 0 check yes timestep 0.00025 fix 1 all nve fix 2 all latte NULL fix_modify 2 energy yes thermo_style custom step temp pe etotal press # dynamics thermo 10 run 10 Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2 ghost atom cutoff = 2 binsize = 1, bins = 20 13 12 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair zero, perpetual attributes: half, newton on pair build: half/bin/newton/tri stencil: half/bin/3d/newton/tri bin: standard Per MPI rank memory allocation (min/avg/max) = 5.651 | 5.651 | 5.651 Mbytes Step Temp PotEng TotEng Press 0 0 -23.980353 -23.980353 348.02716 10 19.123149 -23.990297 -23.98041 18.774332 Loop time of 0.0415399 on 1 procs for 10 steps with 5 atoms Performance: 5.200 ns/day, 4.616 hours/ns, 240.732 timesteps/s 6674.9% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.722e-06 | 5.722e-06 | 5.722e-06 | 0.0 | 0.01 Bond | 7.6294e-06 | 7.6294e-06 | 7.6294e-06 | 0.0 | 0.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 1.8358e-05 | 1.8358e-05 | 1.8358e-05 | 0.0 | 0.04 Output | 2.0981e-05 | 2.0981e-05 | 2.0981e-05 | 0.0 | 0.05 Modify | 0.041394 | 0.041394 | 0.041394 | 0.0 | 99.65 Other | | 9.322e-05 | | | 0.22 Nlocal: 5 ave 5 max 5 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7 ave 7 max 7 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 10 ave 10 max 10 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 10 Ave neighs/atom = 2 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 Total wall time: 0:00:01
lib/latte/Install.py +27 −4 Original line number Diff line number Diff line Loading @@ -4,7 +4,7 @@ # used to automate the steps described in the README file in this dir from __future__ import print_function import sys,os,re,subprocess import sys,os,re,subprocess,hashlib # help message Loading @@ -24,7 +24,7 @@ specify one or more options, order does not matter -b = download and build the LATTE library -p = specify folder of existing LATTE installation -m = copy Makefile.lammps.suffix to Makefile.lammps -v = set version of LATTE library to download and set up (default = 1.1.1) -v = set version of LATTE library to download and set up (default = 1.2.1) Example: Loading @@ -36,6 +36,13 @@ make lib-latte args="-p $HOME/latte" # use existing LATTE installation version = '1.2.1' # known checksums for different LATTE versions. used to validate the download. checksums = { \ '1.1.0' : '533635721ee222d0ed2925a18fb5b294', \ '1.2.0' : '68bf0db879da5e068a71281020239ae7', \ '1.2.1' : 'bed76e7e76c545c36dd848a8f1fd35eb' \ } # print error message or help def error(str=None): Loading Loading @@ -91,6 +98,17 @@ def geturl(url,fname): error("Failed to download source code with 'curl' or 'wget'") return def checkmd5sum(md5sum,fname): with open(fname,'rb') as fh: m = hashlib.md5() while True: data = fh.read(81920) if not data: break m.update(data) fh.close() return m.hexdigest() == md5sum # parse args args = sys.argv[1:] Loading Loading @@ -144,7 +162,12 @@ if buildflag: print("Downloading LATTE ...") geturl(url,"LATTE.tar.gz") print("Unpacking LATTE zipfile ...") # verify downloaded archive integrity via md5 checksum, if known. if version in checksums: if not checkmd5sum(checksums[version],'LATTE.tar.gz'): error("Checksum for LATTE library does not match") print("Unpacking LATTE ...") if os.path.exists(lattedir): cmd = 'rm -rf "%s"' % lattedir subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) Loading
