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This commit is contained in:
Axel Kohlmeyer
2021-07-09 16:54:00 -04:00
parent 46d5d9724a
commit 6571a84884
152 changed files with 39 additions and 67 deletions
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64
examples/PACKAGES/addtorque/in.addtorque Normal file
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units lj
lattice fcc 0.8442
boundary f f f
region ball sphere 0.0 0.0 0.0 5.0
region box block -10 10 -10 10 -10 10
region half block -10 0 -10 10 -10 10
# add molecule ids so we can use chunk/atom
fix 0 all property/atom mol ghost yes
create_box 2 box
create_atoms 1 region ball
pair_style lj/cut 4.0
pair_coeff * * 1.0 1.0
mass * 1.0
set group all mol 1
# label half the sphere with a different type for better visualization
set region half type 2
# use a dynamic group (may require a patch to fix addtorque with older versions of LAMMPS)
group ball dynamic all region ball
neigh_modify delay 2 every 1 check yes
minimize 0.0 0.0 1000 10000
reset_timestep 0
velocity all create 1.2 12351235
fix 1 all nve
fix 2 all wall/reflect xlo EDGE xhi EDGE ylo EDGE yhi EDGE zlo EDGE zhi EDGE
compute 1 all chunk/atom molecule
compute 2 ball omega/chunk 1
compute 3 ball inertia/chunk 1
# compute rotational kinetic energy: 1/2 * I * omega**2
variable r_ke_x equal c_2[1][1]*c_2[1][1]*c_3[1][1]*0.5
variable r_ke_y equal c_2[1][2]*c_2[1][2]*c_3[1][2]*0.5
variable r_ke_z equal c_2[1][3]*c_2[1][3]*c_3[1][3]*0.5
# output moments of inertia for x,y,z and angular velocity as well as rotational kinertic energy
thermo_style custom step ke pe c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z
thermo 500
# dump 1 all atom 100 dump.lammpstrj
# dump 2 all movie 10 ball.mp4 type mass
# equilibration w/o torque added
run 1000 post no
# start spinning the ball. rotation around z should increase and Erot_z should grow
fix 4 ball addtorque 0.0 0.0 200.0
run 10000 upto post no
# continue without adding more torque. rotation continues at fixed speed
unfix 4
run 5000

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examples/PACKAGES/addtorque/log.9Nov16.addtorque.g++.1 Normal file
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LAMMPS (9 Nov 2016)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
units lj
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
boundary f f f
region ball sphere 0.0 0.0 0.0 5.0
region box block -10 10 -10 10 -10 10
region half block -10 0 -10 10 -10 10
# add molecule ids so we can use chunk/atom
fix 0 all property/atom mol ghost yes
create_box 2 box
Created orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid
create_atoms 1 region ball
Created 2123 atoms
pair_style lj/cut 4.0
pair_coeff * * 1.0 1.0
mass * 1.0
set group all mol 1
2123 settings made for mol
# label half the sphere with a different type for better visualization
set region half type 2
1142 settings made for type
# use a dynamic group (may require a patch to fix addtorque with older versions of LAMMPS)
group ball dynamic all region ball
dynamic group ball defined
neigh_modify delay 2 every 1 check yes
minimize 0.0 0.0 1000 10000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.3
ghost atom cutoff = 4.3
binsize = 2.15 -> bins = 16 16 16
Memory usage per processor = 3.68322 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -6.2285099 0 -6.2285099 -0.38871568
1000 0 -7.3616908 0 -7.3616908 -9.1828951e-16
Loop time of 12.4181 on 1 procs for 1000 steps with 2123 atoms
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-6.22850993032 -7.36169083402 -7.36169083402
Force two-norm initial, final = 197.762 3.3539e-12
Force max component initial, final = 7.88704 1.52475e-13
Final line search alpha, max atom move = 1 1.52475e-13
Iterations, force evaluations = 1000 1994
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 12.282 | 12.282 | 12.282 | 0.0 | 98.91
Neigh | 0.06315 | 0.06315 | 0.06315 | 0.0 | 0.51
Comm | 0.000443 | 0.000443 | 0.000443 | 0.0 | 0.00
Output | 2.7e-05 | 2.7e-05 | 2.7e-05 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.07231 | | | 0.58
Nlocal: 2123 ave 2123 max 2123 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 270799 ave 270799 max 270799 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 270799
Ave neighs/atom = 127.555
Neighbor list builds = 11
Dangerous builds = 0
reset_timestep 0
velocity all create 1.2 12351235
fix 1 all nve
fix 2 all wall/reflect xlo EDGE xhi EDGE ylo EDGE yhi EDGE zlo EDGE zhi EDGE
compute 1 all chunk/atom molecule
compute 2 ball omega/chunk 1
compute 3 ball inertia/chunk 1
# compute rotational kinetic energy: 1/2 * I * omega**2
variable r_ke_x equal c_2[1][1]*c_2[1][1]*c_3[1][1]*0.5
variable r_ke_y equal c_2[1][2]*c_2[1][2]*c_3[1][2]*0.5
variable r_ke_z equal c_2[1][3]*c_2[1][3]*c_3[1][3]*0.5
# output moments of inertia for x,y,z and angular velocity as well as rotational kinertic energy
thermo_style custom step ke pe c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z
thermo 500
# dump 1 all atom 100 dump.lammpstrj
# dump 2 all movie 10 ball.mp4 type mass
# equilibration w/o torque added
run 1000 post no
WARNING: One or more dynamic groups may not be updated at correct point in timestep (../fix_group.cpp:153)
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 2 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.3
ghost atom cutoff = 4.3
binsize = 2.15 -> bins = 16 16 16
Memory usage per processor = 2.68359 Mbytes
Step KinEng PotEng c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z
0 1.7991521 -7.3616908 51125.265 51125.265 51125.265 0.0034331372 -0.0045852283 0.0091015032 0.30129221 0.53743693 2.117541
500 0.8882476 -6.43927 52585.112 52205.936 52112.109 0.0033058719 -0.0043753253 0.0089502237 0.2873458 0.49970143 2.0872595
1000 0.79407357 -6.337372 53754.145 54093.977 53787.624 0.0033214912 -0.0042125031 0.0090171557 0.29651603 0.47995375 2.1867116
Loop time of 4.26119 on 1 procs for 1000 steps with 2123 atoms
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
# start spinning the ball. rotation around z should increase and Erot_z should grow
fix 4 ball addtorque 0.0 0.0 200.0
run 10000 upto post no
WARNING: One or more dynamic groups may not be updated at correct point in timestep (../fix_group.cpp:153)
Memory usage per processor = 2.68359 Mbytes
Step KinEng PotEng c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z
1000 0.79407357 -6.337372 53754.145 54093.977 53787.624 0.0033214912 -0.0042125031 0.0090171557 0.29651603 0.47995375 2.1867116
1500 0.68685306 -6.2226287 55026.889 54809.958 55224.858 0.0026096779 -0.0039390202 0.01797948 0.18737807 0.42521238 8.9260406
2000 0.65370325 -6.1832475 54914.897 55655.542 55405.781 0.0029310978 -0.0040761978 0.025816421 0.23589612 0.46236922 18.463634
2500 0.69337585 -6.2170462 54604.66 54800.001 54488.865 0.0028821313 -0.0045216915 0.035781895 0.22679174 0.56021203 34.882245
3000 0.76778067 -6.2850756 53423.198 53620.349 53692.133 0.004088872 -0.004451787 0.044703139 0.44658786 0.53133496 53.64839
3500 0.79707238 -6.3044974 53055.225 53071.129 52927.537 0.0036751739 -0.0037584362 0.054889715 0.3583059 0.3748372 79.732181
4000 0.80746429 -6.3010044 53519.853 53643.284 54058.105 0.003813517 -0.0041637733 0.062983015 0.38916725 0.46500703 107.22047
4500 0.81206394 -6.2884719 53371.354 53883.202 53854.559 0.00385001 -0.003643712 0.072544638 0.39555051 0.35769386 141.71085
5000 0.81648687 -6.2737414 53776.764 54233.367 53762.425 0.0024484228 -0.0043310965 0.080673643 0.16118978 0.50866551 174.94929
5500 0.81888245 -6.2572796 53908.22 53502.342 54717.506 0.0037110524 -0.00327586 0.088836946 0.37120958 0.28707375 215.91536
6000 0.86533749 -6.2804248 53687.533 53571.135 53536.171 0.0025223465 -0.0047753224 0.099646475 0.17078626 0.61081016 265.79156
6500 0.88029206 -6.2719195 53344.67 53291.068 53298.665 0.003937416 -0.0033910578 0.10778737 0.41350774 0.30640427 309.61504
7000 0.9066019 -6.2714707 53928.646 53524.142 54003.175 0.0028500736 -0.0039730774 0.11855069 0.21902903 0.4224485 379.4875
7500 0.94601421 -6.2819912 53534.525 53547.598 53851.344 0.0028610722 -0.0049440438 0.12716472 0.21910969 0.6544472 435.41142
8000 0.9562253 -6.2626222 53486.577 53033.175 53858.803 0.0025501008 -0.0048075887 0.13526164 0.17391198 0.61287549 492.69254
8500 0.99679401 -6.2691139 53566.766 53721.523 53831.283 0.0034137155 -0.0039265 0.14392854 0.3121189 0.41412316 557.56894
9000 1.0371056 -6.2761647 53415.879 53605.078 53985.02 0.0029321914 -0.0046362889 0.1518846 0.2296281 0.57612526 622.6884
9500 1.0598491 -6.26216 53493.003 53049.859 53699.774 0.0032127038 -0.0050624912 0.16002437 0.27606311 0.67980256 687.56651
10000 1.1014855 -6.2654945 53418.49 53251.964 53867.56 0.0037330249 -0.0056278017 0.17103133 0.37220602 0.84330216 787.85924
Loop time of 43.025 on 1 procs for 9000 steps with 2123 atoms
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
# continue without adding more torque. rotation continues at fixed speed
unfix 4
run 5000
WARNING: One or more dynamic groups may not be updated at correct point in timestep (../fix_group.cpp:153)
Memory usage per processor = 2.68359 Mbytes
Step KinEng PotEng c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z
10000 1.1014855 -6.2654945 53418.49 53251.964 53867.56 0.0037330249 -0.0056278017 0.17103133 0.37220602 0.84330216 787.85924
10500 1.07259 -6.2363698 52825.233 52896.327 55753.551 0.0035928335 -0.0050843805 0.16344484 0.34094601 0.68370948 744.70621
11000 1.0644214 -6.2282099 52016.795 51950.497 54922.101 0.0047316668 -0.0050149935 0.16196531 0.58229343 0.65328165 720.37919
11500 1.0887339 -6.2525622 52602.789 52903.594 54461.53 0.0044295697 -0.0046710153 0.16698036 0.51606197 0.57713546 759.26022
12000 1.0707466 -6.234719 52785.654 52997.192 54943.066 0.0057389353 -0.0030340721 0.16553451 0.86925773 0.2439353 752.76594
12500 1.0758302 -6.2397291 52375.734 52783.309 55011.986 0.0047029783 -0.0023526884 0.16493895 0.57922337 0.14608158 748.29657
13000 1.0716957 -6.2354221 52711.183 52788.224 55234.737 0.0034033406 -0.00206283 0.16427569 0.30526962 0.11231401 745.29615
13500 1.083667 -6.2475953 52698.902 52203.324 55102.881 0.0032012254 -0.0021366488 0.16381832 0.27002507 0.11916109 739.38261
14000 1.085106 -6.2490655 52767.613 52353.974 55225.438 0.0025647931 -0.0022235227 0.1636534 0.17355699 0.12942041 739.53587
14500 1.0838261 -6.2477856 52292.343 51995.567 54735.836 0.001794954 -0.0029396951 0.16409339 0.084239299 0.22466783 736.92607
15000 1.0827419 -6.2468971 51917.584 51388.833 54481.681 0.0017979486 -0.0025793756 0.16196568 0.083914884 0.17094953 714.60575
Loop time of 22.7848 on 1 procs for 5000 steps with 2123 atoms
Performance: 94800.138 tau/day, 219.445 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 18.891 | 18.891 | 18.891 | 0.0 | 82.91
Neigh | 3.5735 | 3.5735 | 3.5735 | 0.0 | 15.68
Comm | 0.005778 | 0.005778 | 0.005778 | 0.0 | 0.03
Output | 0.001862 | 0.001862 | 0.001862 | 0.0 | 0.01
Modify | 0.27476 | 0.27476 | 0.27476 | 0.0 | 1.21
Other | | 0.0379 | | | 0.17
Nlocal: 2123 ave 2123 max 2123 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 242472 ave 242472 max 242472 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 242472
Ave neighs/atom = 114.212
Neighbor list builds = 560
Dangerous builds = 0
Total wall time: 0:01:22

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LAMMPS (9 Nov 2016)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
units lj
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
boundary f f f
region ball sphere 0.0 0.0 0.0 5.0
region box block -10 10 -10 10 -10 10
region half block -10 0 -10 10 -10 10
# add molecule ids so we can use chunk/atom
fix 0 all property/atom mol ghost yes
create_box 2 box
Created orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid
create_atoms 1 region ball
Created 2123 atoms
pair_style lj/cut 4.0
pair_coeff * * 1.0 1.0
mass * 1.0
set group all mol 1
2123 settings made for mol
# label half the sphere with a different type for better visualization
set region half type 2
1142 settings made for type
# use a dynamic group (may require a patch to fix addtorque with older versions of LAMMPS)
group ball dynamic all region ball
dynamic group ball defined
neigh_modify delay 2 every 1 check yes
minimize 0.0 0.0 1000 10000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.3
ghost atom cutoff = 4.3
binsize = 2.15 -> bins = 16 16 16
Memory usage per processor = 3.77014 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -6.2285099 0 -6.2285099 -0.38871568
1000 0 -7.3616908 0 -7.3616908 -9.7399049e-16
Loop time of 8.29581 on 4 procs for 1000 steps with 2123 atoms
89.4% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-6.22850993032 -7.36169083402 -7.36169083402
Force two-norm initial, final = 197.762 3.40861e-12
Force max component initial, final = 7.88704 1.60379e-13
Final line search alpha, max atom move = 1 1.60379e-13
Iterations, force evaluations = 1000 1994
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.8462 | 6.8198 | 8.0872 | 34.0 | 82.21
Neigh | 0.021211 | 0.028936 | 0.035891 | 3.8 | 0.35
Comm | 0.10672 | 1.3842 | 2.3694 | 76.2 | 16.69
Output | 2.8e-05 | 3.35e-05 | 5e-05 | 0.2 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0629 | | | 0.76
Nlocal: 530.75 ave 543 max 514 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Nghost: 1058.25 ave 1075 max 1046 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Neighs: 67699.8 ave 82013 max 55681 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Total # of neighbors = 270799
Ave neighs/atom = 127.555
Neighbor list builds = 11
Dangerous builds = 0
reset_timestep 0
velocity all create 1.2 12351235
fix 1 all nve
fix 2 all wall/reflect xlo EDGE xhi EDGE ylo EDGE yhi EDGE zlo EDGE zhi EDGE
compute 1 all chunk/atom molecule
compute 2 ball omega/chunk 1
compute 3 ball inertia/chunk 1
# compute rotational kinetic energy: 1/2 * I * omega**2
variable r_ke_x equal c_2[1][1]*c_2[1][1]*c_3[1][1]*0.5
variable r_ke_y equal c_2[1][2]*c_2[1][2]*c_3[1][2]*0.5
variable r_ke_z equal c_2[1][3]*c_2[1][3]*c_3[1][3]*0.5
# output moments of inertia for x,y,z and angular velocity as well as rotational kinertic energy
thermo_style custom step ke pe c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z
thermo 500
# dump 1 all atom 100 dump.lammpstrj
# dump 2 all movie 10 ball.mp4 type mass
# equilibration w/o torque added
run 1000 post no
WARNING: One or more dynamic groups may not be updated at correct point in timestep (../fix_group.cpp:153)
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 2 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.3
ghost atom cutoff = 4.3
binsize = 2.15 -> bins = 16 16 16
Memory usage per processor = 2.77052 Mbytes
Step KinEng PotEng c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z
0 1.7991521 -7.3616908 51125.265 51125.265 51125.265 0.0040198435 -0.0024237256 0.0011306245 0.4130702 0.15016629 0.032677011
500 0.90968729 -6.4603004 52559.075 52593.598 52370.876 0.0039073429 -0.0023505431 0.0011032256 0.40121833 0.14529121 0.031870471
1000 0.80269935 -6.3456699 53966.859 54192.03 54298.931 0.0040875347 -0.0023098179 0.00077010445 0.45083753 0.14456425 0.016101285
Loop time of 2.3842 on 4 procs for 1000 steps with 2123 atoms
89.0% CPU use with 4 MPI tasks x 1 OpenMP threads
# start spinning the ball. rotation around z should increase and Erot_z should grow
fix 4 ball addtorque 0.0 0.0 200.0
run 10000 upto post no
WARNING: One or more dynamic groups may not be updated at correct point in timestep (../fix_group.cpp:153)
Memory usage per processor = 2.77052 Mbytes
Step KinEng PotEng c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z
1000 0.80269935 -6.3456699 53966.859 54192.03 54298.931 0.0040875347 -0.0023098179 0.00077010445 0.45083753 0.14456425 0.016101285
1500 0.68922642 -6.2266953 54966.109 54681.607 54947.256 0.0038798951 -0.0016325797 0.0099837591 0.41371853 0.072871893 2.7384461
2000 0.64105167 -6.1739656 54782.995 54570.486 54910.316 0.0034645832 -0.0027243304 0.017763588 0.32878936 0.20251043 8.6633395
2500 0.69929409 -6.2287557 54307.47 53952.925 54538.409 0.0035199565 -0.0022538001 0.028279733 0.33643732 0.13703004 21.808363
3000 0.77013056 -6.2945597 53916.743 53801.81 53955.863 0.0039732989 -0.0024543292 0.037182149 0.42559463 0.16204384 37.297319
3500 0.80807105 -6.3246605 53451.163 53387.178 53474.789 0.0043137676 -0.0020556348 0.047270147 0.49732542 0.11279735 59.743821
4000 0.81007199 -6.3142362 53334.317 53243.089 53685.963 0.0038548696 -0.0031009535 0.055811043 0.3962745 0.25599044 83.612467
4500 0.7850954 -6.2735818 53738.002 53682.367 53639.471 0.0033046861 -0.0018472801 0.065975851 0.29343502 0.091594032 116.74129
5000 0.77992741 -6.2508277 53864.644 53804.867 53877.025 0.0038258186 -0.0028703189 0.073848203 0.39420539 0.2216419 146.91071
5500 0.79428302 -6.2467907 54353.329 53987.578 54234.062 0.0034715133 -0.0030161617 0.082746129 0.32751699 0.24556875 185.66819
6000 0.82211943 -6.2549436 54273.545 53195.299 54061.645 0.0030929934 -0.0031282112 0.090458895 0.25960687 0.26027676 221.18813
6500 0.87630771 -6.2870988 54042.229 53505.982 54492.239 0.0026486452 -0.0024783378 0.10046947 0.18956181 0.1643211 275.02546
7000 0.88614639 -6.2727488 53701.993 52682.206 53948.142 0.0035384498 -0.0035905797 0.11030427 0.33619131 0.33959641 328.19439
7500 0.92102182 -6.2787281 53410.068 52577.853 53132.511 0.0033084315 -0.0031776605 0.11973875 0.2923058 0.26545312 380.8902
8000 0.94010525 -6.2697758 53732.562 53384.271 53795.933 0.0046460009 -0.0032755993 0.12803006 0.5799174 0.28639462 440.90328
8500 0.95359399 -6.252319 53444.305 53558.444 53789.691 0.0037919474 -0.0035729209 0.13616177 0.38423423 0.34185722 498.63117
9000 0.98631627 -6.25197 53115.01 54017.327 53955.578 0.0045084495 -0.0034368377 0.14488919 0.53981096 0.31902236 566.34143
9500 1.0328238 -6.2632597 53287.675 53682.978 53769.692 0.0044595175 -0.0025931203 0.15416363 0.5298739 0.1804895 638.95665
10000 1.0741755 -6.2667785 53103.657 53319.569 53601.523 0.0059237675 -0.0019561182 0.16445664 0.93173079 0.10201096 724.85302
Loop time of 21.8398 on 4 procs for 9000 steps with 2123 atoms
90.3% CPU use with 4 MPI tasks x 1 OpenMP threads
# continue without adding more torque. rotation continues at fixed speed
unfix 4
run 5000
WARNING: One or more dynamic groups may not be updated at correct point in timestep (../fix_group.cpp:153)
Memory usage per processor = 2.77052 Mbytes
Step KinEng PotEng c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z
10000 1.0741755 -6.2667785 53103.657 53319.569 53601.523 0.0059237675 -0.0019561182 0.16445664 0.93173079 0.10201096 724.85302
10500 1.0588571 -6.2509381 52374.303 52131.544 55020.367 0.0048843769 -0.0018716797 0.15729531 0.62475047 0.091313217 680.65188
11000 1.0554911 -6.2471863 52803.345 52177.891 55200.756 0.0042073234 -0.0024283269 0.15742315 0.46735107 0.15384055 683.99392
11500 1.0559499 -6.2469955 54031.351 52919.728 54882.35 0.0046703444 -0.0016225764 0.15994353 0.58926908 0.06966232 701.99832
12000 1.0311805 -6.2224471 52812.51 52444.13 55356.101 0.0044986993 -0.0019225732 0.15672327 0.53441759 0.096924293 679.83334
12500 1.0423882 -6.2339087 52000.562 52043.013 55003.272 0.0038688875 -0.0022935053 0.1548654 0.38917977 0.13687746 659.57977
13000 1.0548857 -6.2465445 52196.499 52869.024 54622.553 0.0036650563 -0.0025542156 0.1590498 0.35056832 0.17245921 690.88895
13500 1.0443009 -6.2360149 51921.746 53124.078 54750.325 0.0052756473 -0.0011658069 0.15689119 0.72255483 0.036100621 673.83538
14000 1.0505583 -6.241923 51861.696 52153.234 54321.531 0.0037119391 -0.00045576703 0.15738082 0.35728798 0.0054167284 672.73745
14500 1.040343 -6.2316147 52035.588 51680.479 54443.305 0.0026177168 -0.0014795729 0.15428968 0.1782854 0.056567797 648.01978
15000 1.0404962 -6.2322338 52376.795 51327.453 54677.693 0.0025711787 -0.0021695312 0.15403509 0.17313044 0.12079571 648.66363
Loop time of 11.9695 on 4 procs for 5000 steps with 2123 atoms
Performance: 180458.440 tau/day, 417.728 timesteps/s
89.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.0313 | 8.4017 | 9.6932 | 35.5 | 70.19
Neigh | 0.97886 | 1.3633 | 1.7406 | 26.8 | 11.39
Comm | 0.34002 | 2.0227 | 3.7911 | 94.9 | 16.90
Output | 0.001198 | 0.0015522 | 0.002578 | 1.5 | 0.01
Modify | 0.12841 | 0.131 | 0.13336 | 0.5 | 1.09
Other | | 0.04924 | | | 0.41
Nlocal: 530.75 ave 534 max 529 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Nghost: 1038 ave 1048 max 1029 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 60482.5 ave 72547 max 49124 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Total # of neighbors = 241930
Ave neighs/atom = 113.957
Neighbor list builds = 555
Dangerous builds = 0
Total wall time: 0:00:44

413
examples/PACKAGES/gle/data.h2o-quantum Normal file
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LAMMPS data file. CGCMM style. atom_style full generated by VMD/TopoTools v1.4 on Tue Aug 05 00:34:49 EDT 2014
192 atoms
128 bonds
64 angles
0 dihedrals
0 impropers
2 atom types
1 bond types
1 angle types
0 dihedral types
0 improper types
-0.025952 12.398448 xlo xhi
-0.072222 12.352178 ylo yhi
0.103767 12.528167 zlo zhi
Masses
1 15.999400 # O
2 1.008000 # H
Atoms # full
1 1 1 -1.112800 11.904200 11.004000 2.647150 # O
2 1 2 0.556400 11.274600 10.441300 3.165040 # H
3 1 2 0.556400 12.657229 10.697500 2.992120 # H
4 2 1 -1.112800 11.419600 1.182280 9.137010 # O
5 2 2 0.556400 11.398800 1.594150 8.310830 # H
6 2 2 0.556400 10.506300 0.898235 9.233160 # H
7 3 1 -1.112800 4.826680 1.783510 11.516400 # O
8 3 2 0.556400 4.546870 1.811150 10.564300 # H
9 3 2 0.556400 4.055660 1.238270 11.973500 # H
10 4 1 -1.112800 12.288000 1.904120 1.044200 # O
11 4 2 0.556400 11.828600 1.153600 0.839629 # H
12 4 2 0.556400 12.277700 2.333890 0.302505 # H
13 5 1 -1.112800 11.857500 1.676770 6.187920 # O
14 5 2 0.556400 11.648400 2.074730 5.284650 # H
15 5 2 0.556400 11.876700 0.812108 5.948150 # H
16 6 1 -1.112800 2.097890 5.057070 3.011100 # O
17 6 2 0.556400 2.136570 4.204340 2.822200 # H
18 6 2 0.556400 1.248920 5.503130 3.095170 # H
19 7 1 -1.112800 8.969570 9.662130 12.397100 # O
20 7 2 0.556400 9.686170 10.151600 12.437590 # H
21 7 2 0.556400 9.532380 8.853020 12.470100 # H
22 8 1 -1.112800 7.003800 0.166948 11.866400 # O
23 8 2 0.556400 7.602080 -0.008490 11.078100 # H
24 8 2 0.556400 6.314920 0.854812 11.845400 # H
25 9 1 -1.112800 7.279490 7.009030 4.039650 # O
26 9 2 0.556400 6.480970 6.584280 4.507850 # H
27 9 2 0.556400 7.966830 6.725300 4.670490 # H
28 10 1 -1.112800 4.968300 6.252330 2.294100 # O
29 10 2 0.556400 4.323490 6.517690 2.931870 # H
30 10 2 0.556400 5.091090 6.970190 1.641050 # H
31 11 1 -1.112800 9.233370 1.170670 1.198800 # O
32 11 2 0.556400 8.772080 2.002300 1.423460 # H
33 11 2 0.556400 8.648900 0.665205 0.687128 # H
34 12 1 -1.112800 10.128900 4.638490 3.506180 # O
35 12 2 0.556400 9.350580 4.298580 3.037750 # H
36 12 2 0.556400 9.946100 4.618830 4.531850 # H
37 13 1 -1.112800 2.868470 0.334175 0.677477 # O
38 13 2 0.556400 2.403840 0.200999 -0.138964 # H
39 13 2 0.556400 2.069790 0.770509 1.118620 # H
40 14 1 -1.112800 0.990607 8.880780 7.919540 # O
41 14 2 0.556400 1.468800 8.257450 8.474370 # H
42 14 2 0.556400 1.548730 9.628320 7.837180 # H
43 15 1 -1.112800 6.037680 11.965300 1.967580 # O
44 15 2 0.556400 6.711200 11.358900 2.192700 # H
45 15 2 0.556400 6.440020 12.350600 1.125540 # H
46 16 1 -1.112800 10.081700 7.285330 11.995600 # O
47 16 2 0.556400 9.502260 6.951850 12.805980 # H
48 16 2 0.556400 9.656250 6.986780 11.119000 # H
49 17 1 -1.112800 8.035030 3.368010 1.956490 # O
50 17 2 0.556400 7.178750 3.084810 2.288990 # H
51 17 2 0.556400 7.710830 4.079910 1.281810 # H
52 18 1 -1.112800 6.425050 9.669080 5.164110 # O
53 18 2 0.556400 5.437580 9.502120 5.160280 # H
54 18 2 0.556400 6.816230 9.186900 4.533480 # H
55 19 1 -1.112800 5.379420 6.514400 8.405390 # O
56 19 2 0.556400 5.755950 6.334530 9.297210 # H
57 19 2 0.556400 5.440740 7.514240 8.532830 # H
58 20 1 -1.112800 2.046140 1.943010 5.846200 # O
59 20 2 0.556400 1.143970 1.913690 6.058140 # H
60 20 2 0.556400 2.248230 1.154690 5.418870 # H
61 21 1 -1.112800 5.107140 1.201150 4.136430 # O
62 21 2 0.556400 5.044840 2.013910 3.551730 # H
63 21 2 0.556400 5.377520 0.578867 3.455080 # H
64 22 1 -1.112800 4.596620 8.523380 10.800400 # O
65 22 2 0.556400 5.239180 8.321920 11.448900 # H
66 22 2 0.556400 3.811110 8.904250 11.215900 # H
67 23 1 -1.112800 11.753800 2.360940 3.561900 # O
68 23 2 0.556400 11.219800 3.198640 3.682850 # H
69 23 2 0.556400 11.740900 2.309440 2.589890 # H
70 24 1 -1.112800 10.148400 9.230600 4.794850 # O
71 24 2 0.556400 10.724900 8.587640 4.193460 # H
72 24 2 0.556400 9.774880 8.755770 5.473800 # H
73 25 1 -1.112800 3.678800 8.862530 5.475880 # O
74 25 2 0.556400 3.654050 7.908400 5.269890 # H
75 25 2 0.556400 3.784180 9.231390 6.370230 # H
76 26 1 -1.112800 2.424500 5.061670 0.010513 # O
77 26 2 0.556400 2.259390 5.063060 1.073770 # H
78 26 2 0.556400 1.699730 5.358760 -0.532400 # H
79 27 1 -1.112800 2.031790 9.273860 3.335100 # O
80 27 2 0.556400 2.576050 9.625000 2.421210 # H
81 27 2 0.556400 2.552020 9.204230 4.251920 # H
82 28 1 -1.112800 0.671121 5.562010 10.459300 # O
83 28 2 0.556400 0.240613 4.699610 10.429400 # H
84 28 2 0.556400 1.201350 5.761520 9.675160 # H
85 29 1 -1.112800 2.186950 2.475840 2.653370 # O
86 29 2 0.556400 2.318520 2.024870 3.544650 # H
87 29 2 0.556400 1.317700 2.072840 2.368920 # H
88 30 1 -1.112800 2.189580 6.283080 8.069060 # O
89 30 2 0.556400 1.900250 6.315140 7.216860 # H
90 30 2 0.556400 3.129850 6.506460 8.013540 # H
91 31 1 -1.112800 8.673330 10.156400 9.670670 # O
92 31 2 0.556400 8.580570 10.190500 10.546700 # H
93 31 2 0.556400 9.689670 10.206300 9.469020 # H
94 32 1 -1.112800 3.925400 3.636840 7.691570 # O
95 32 2 0.556400 4.254210 4.458460 7.545880 # H
96 32 2 0.556400 2.917900 3.558790 7.218470 # H
97 33 1 -1.112800 2.091950 11.573700 5.309100 # O
98 33 2 0.556400 2.360650 10.852800 4.677420 # H
99 33 2 0.556400 1.246180 11.339800 5.622280 # H
100 34 1 -1.112800 9.475430 0.348874 4.098120 # O
101 34 2 0.556400 8.884690 -0.244864 3.347450 # H
102 34 2 0.556400 10.054100 0.774503 3.600670 # H
103 35 1 -1.112800 0.010520 6.679330 6.084480 # O
104 35 2 0.556400 0.046652 7.214860 6.876490 # H
105 35 2 0.556400 0.310100 7.241510 5.330880 # H
106 36 1 -1.112800 6.153230 4.948680 5.715680 # O
107 36 2 0.556400 6.347170 5.425750 6.507980 # H
108 36 2 0.556400 6.681400 4.134080 5.619610 # H
109 37 1 -1.112800 3.898970 10.122100 1.533400 # O
110 37 2 0.556400 4.479990 10.910500 1.499800 # H
111 37 2 0.556400 3.858400 10.101700 0.579605 # H
112 38 1 -1.112800 11.506200 3.204840 10.861000 # O
113 38 2 0.556400 10.597600 3.222960 11.028100 # H
114 38 2 0.556400 11.546500 2.434670 10.319100 # H
115 39 1 -1.112800 10.677900 4.338840 6.172880 # O
116 39 2 0.556400 11.342100 4.987790 6.277110 # H
117 39 2 0.556400 11.105000 3.454520 6.329560 # H
118 40 1 -1.112800 11.269000 10.402200 8.967430 # O
119 40 2 0.556400 11.945700 9.669490 8.817430 # H
120 40 2 0.556400 11.392200 10.972400 9.673550 # H
121 41 1 -1.112800 9.015520 6.819390 9.590060 # O
122 41 2 0.556400 8.480310 7.447960 9.075890 # H
123 41 2 0.556400 8.772660 5.864390 9.537090 # H
124 42 1 -1.112800 9.156080 7.043630 6.079910 # O
125 42 2 0.556400 9.786990 6.368220 6.462160 # H
126 42 2 0.556400 8.637950 7.287850 6.807400 # H
127 43 1 -1.112800 8.023320 10.118300 2.593470 # O
128 43 2 0.556400 8.835280 9.772450 3.075270 # H
129 43 2 0.556400 8.319480 10.174900 1.654080 # H
130 44 1 -1.112800 11.458700 11.363500 6.215150 # O
131 44 2 0.556400 10.817600 10.742100 5.830830 # H
132 44 2 0.556400 11.362800 11.032500 7.071230 # H
133 45 1 -1.112800 7.501170 8.687200 7.619310 # O
134 45 2 0.556400 6.987900 9.210670 6.875940 # H
135 45 2 0.556400 7.775980 9.294880 8.278630 # H
136 46 1 -1.112800 12.163200 7.636940 3.306910 # O
137 46 2 0.556400 11.905500 7.001590 2.634400 # H
138 46 2 0.556400 13.143695 7.878660 3.172600 # H
139 47 1 -1.112800 3.855820 9.856260 8.038060 # O
140 47 2 0.556400 4.106300 10.648500 7.785770 # H
141 47 2 0.556400 4.004960 10.015200 9.060490 # H
142 48 1 -1.112800 11.959100 11.106700 12.207400 # O
143 48 2 0.556400 11.627900 11.064000 13.164333 # H
144 48 2 0.556400 12.908351 10.710100 12.287100 # H
145 49 1 -1.112800 5.215880 4.825910 11.379400 # O
146 49 2 0.556400 5.091530 3.935540 11.648000 # H
147 49 2 0.556400 4.395040 5.172330 11.674300 # H
148 50 1 -1.112800 3.447470 6.263900 5.322950 # O
149 50 2 0.556400 2.953140 6.002480 4.629230 # H
150 50 2 0.556400 4.256030 5.710520 5.184060 # H
151 51 1 -1.112800 9.252860 6.955710 2.103340 # O
152 51 2 0.556400 9.635100 6.201610 2.627900 # H
153 51 2 0.556400 8.511360 7.033430 2.773840 # H
154 52 1 -1.112800 7.010900 2.690190 8.051850 # O
155 52 2 0.556400 7.205340 2.906420 7.186290 # H
156 52 2 0.556400 5.978790 2.609760 8.151220 # H
157 53 1 -1.112800 7.593650 5.241530 12.303700 # O
158 53 2 0.556400 7.778320 6.013730 11.866800 # H
159 53 2 0.556400 6.619420 5.032550 12.146000 # H
160 54 1 -1.112800 8.311930 4.384830 9.775160 # O
161 54 2 0.556400 8.029970 3.742280 9.209050 # H
162 54 2 0.556400 7.710280 4.412850 10.689200 # H
163 55 1 -1.112800 0.216025 8.259980 11.000200 # O
164 55 2 0.556400 -0.771200 8.207870 11.179900 # H
165 55 2 0.556400 0.405663 7.364710 10.808500 # H
166 56 1 -1.112800 5.092650 3.345230 2.380140 # O
167 56 2 0.556400 4.289880 3.402320 2.037290 # H
168 56 2 0.556400 5.195870 4.270950 2.448160 # H
169 57 1 -1.112800 8.415280 0.433228 9.468590 # O
170 57 2 0.556400 8.232370 -0.590000 9.181410 # H
171 57 2 0.556400 7.890330 0.865852 8.788890 # H
172 58 1 -1.112800 1.521980 12.261800 10.252200 # O
173 58 2 0.556400 2.313870 12.717497 9.819640 # H
174 58 2 0.556400 0.740191 12.869956 10.193400 # H
175 59 1 -1.112800 5.046090 0.042758 7.210720 # O
176 59 2 0.556400 4.465450 0.143690 6.438300 # H
177 59 2 0.556400 6.007220 0.148100 6.995730 # H
178 60 1 -1.112800 8.116110 11.951600 6.522740 # O
179 60 2 0.556400 8.877920 11.978800 5.875040 # H
180 60 2 0.556400 7.461260 11.374300 6.175280 # H
181 61 1 -1.112800 7.559250 2.393910 5.322680 # O
182 61 2 0.556400 8.225370 1.772280 4.928820 # H
183 61 2 0.556400 6.701890 2.109310 4.957270 # H
184 62 1 -1.112800 2.306480 9.941070 11.436600 # O
185 62 2 0.556400 1.774970 9.157100 11.271100 # H
186 62 2 0.556400 1.870360 10.613100 10.942200 # H
187 63 1 -1.112800 3.674940 1.236140 9.165420 # O
188 63 2 0.556400 4.256920 0.800629 8.426150 # H
189 63 2 0.556400 3.551770 2.121820 8.663390 # H
190 64 1 -1.112800 6.313260 8.030800 0.560737 # O
191 64 2 0.556400 7.065380 7.786980 0.801491 # H
192 64 2 0.556400 6.039630 8.846740 1.106740 # H
Bonds
1 1 1 2
2 1 1 3
3 1 4 5
4 1 4 6
5 1 7 8
6 1 7 9
7 1 10 11
8 1 10 12
9 1 13 14
10 1 13 15
11 1 16 17
12 1 16 18
13 1 19 20
14 1 19 21
15 1 22 23
16 1 22 24
17 1 25 26
18 1 25 27
19 1 28 29
20 1 28 30
21 1 31 32
22 1 31 33
23 1 34 35
24 1 34 36
25 1 37 38
26 1 37 39
27 1 40 41
28 1 40 42
29 1 43 44
30 1 43 45
31 1 46 47
32 1 46 48
33 1 49 50
34 1 49 51
35 1 52 53
36 1 52 54
37 1 55 56
38 1 55 57
39 1 58 59
40 1 58 60
41 1 61 62
42 1 61 63
43 1 64 65
44 1 64 66
45 1 67 68
46 1 67 69
47 1 70 71
48 1 70 72
49 1 73 74
50 1 73 75
51 1 76 77
52 1 76 78
53 1 79 80
54 1 79 81
55 1 82 83
56 1 82 84
57 1 85 86
58 1 85 87
59 1 88 89
60 1 88 90
61 1 91 92
62 1 91 93
63 1 94 95
64 1 94 96
65 1 97 98
66 1 97 99
67 1 100 101
68 1 100 102
69 1 103 104
70 1 103 105
71 1 106 107
72 1 106 108
73 1 109 110
74 1 109 111
75 1 112 113
76 1 112 114
77 1 115 116
78 1 115 117
79 1 118 119
80 1 118 120
81 1 121 122
82 1 121 123
83 1 124 125
84 1 124 126
85 1 127 128
86 1 127 129
87 1 130 131
88 1 130 132
89 1 133 134
90 1 133 135
91 1 136 137
92 1 136 138
93 1 139 140
94 1 139 141
95 1 142 143
96 1 142 144
97 1 145 146
98 1 145 147
99 1 148 149
100 1 148 150
101 1 151 152
102 1 151 153
103 1 154 155
104 1 154 156
105 1 157 158
106 1 157 159
107 1 160 161
108 1 160 162
109 1 163 164
110 1 163 165
111 1 166 167
112 1 166 168
113 1 169 170
114 1 169 171
115 1 172 173
116 1 172 174
117 1 175 176
118 1 175 177
119 1 178 179
120 1 178 180
121 1 181 182
122 1 181 183
123 1 184 185
124 1 184 186
125 1 187 188
126 1 187 189
127 1 190 191
128 1 190 192
Angles
1 1 2 1 3
2 1 5 4 6
3 1 8 7 9
4 1 11 10 12
5 1 14 13 15
6 1 17 16 18
7 1 20 19 21
8 1 23 22 24
9 1 26 25 27
10 1 29 28 30
11 1 32 31 33
12 1 35 34 36
13 1 38 37 39
14 1 41 40 42
15 1 44 43 45
16 1 47 46 48
17 1 50 49 51
18 1 53 52 54
19 1 56 55 57
20 1 59 58 60
21 1 62 61 63
22 1 65 64 66
23 1 68 67 69
24 1 71 70 72
25 1 74 73 75
26 1 77 76 78
27 1 80 79 81
28 1 83 82 84
29 1 86 85 87
30 1 89 88 90
31 1 92 91 93
32 1 95 94 96
33 1 98 97 99
34 1 101 100 102
35 1 104 103 105
36 1 107 106 108
37 1 110 109 111
38 1 113 112 114
39 1 116 115 117
40 1 119 118 120
41 1 122 121 123
42 1 125 124 126
43 1 128 127 129
44 1 131 130 132
45 1 134 133 135
46 1 137 136 138
47 1 140 139 141
48 1 143 142 144
49 1 146 145 147
50 1 149 148 150
51 1 152 151 153
52 1 155 154 156
53 1 158 157 159
54 1 161 160 162
55 1 164 163 165
56 1 167 166 168
57 1 170 169 171
58 1 173 172 174
59 1 176 175 177
60 1 179 178 180
61 1 182 181 183
62 1 185 184 186
63 1 188 187 189
64 1 191 190 192

413
examples/PACKAGES/gle/data.h2o-smart Normal file
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LAMMPS data file. CGCMM style. atom_style full generated by VMD/TopoTools v1.4 on Tue Aug 05 00:31:12 EDT 2014
192 atoms
128 bonds
64 angles
0 dihedrals
0 impropers
2 atom types
1 bond types
1 angle types
0 dihedral types
0 improper types
-0.160700 12.263700 xlo xhi
0.088670 12.513070 ylo yhi
-0.104992 12.319408 zlo zhi
Masses
1 15.999400 # O
2 1.008000 # H
Atoms # full
1 1 1 -1.112800 8.865130 6.503010 11.121500 # O
2 1 2 0.556400 8.520580 6.510690 12.010700 # H
3 1 2 0.556400 9.732920 6.095080 11.252600 # H
4 2 1 -1.112800 9.057870 9.808280 0.453392 # O
5 2 2 0.556400 8.226490 9.807820 -0.069800 # H
6 2 2 0.556400 9.803510 9.663050 -0.208053 # H
7 3 1 -1.112800 4.233750 5.283420 5.673040 # O
8 3 2 0.556400 3.609940 4.927770 5.028710 # H
9 3 2 0.556400 4.506350 6.135170 5.403380 # H
10 4 1 -1.112800 6.210960 12.255200 3.667540 # O
11 4 2 0.556400 6.203190 12.988556 4.301280 # H
12 4 2 0.556400 5.315370 12.213238 3.274570 # H
13 5 1 -1.112800 6.275240 1.053570 6.253780 # O
14 5 2 0.556400 5.974360 0.104128 6.328520 # H
15 5 2 0.556400 7.171460 1.060860 6.668600 # H
16 6 1 -1.112800 1.413870 8.608640 3.047230 # O
17 6 2 0.556400 1.361670 9.551560 3.309720 # H
18 6 2 0.556400 1.889760 8.168230 3.715680 # H
19 7 1 -1.112800 5.657890 7.278710 0.675859 # O
20 7 2 0.556400 5.220170 6.635890 0.022046 # H
21 7 2 0.556400 4.956600 7.815440 1.121120 # H
22 8 1 -1.112800 4.540490 5.624290 11.350300 # O
23 8 2 0.556400 4.956510 4.796040 11.676400 # H
24 8 2 0.556400 4.750030 5.536620 10.412400 # H
25 9 1 -1.112800 0.035729 6.794620 1.097950 # O
26 9 2 0.556400 0.764984 6.256710 0.729692 # H
27 9 2 0.556400 0.398995 7.264730 1.849450 # H
28 10 1 -1.112800 3.738790 11.789600 2.452560 # O
29 10 2 0.556400 3.256890 11.850800 3.289280 # H
30 10 2 0.556400 3.064120 12.136500 1.778280 # H
31 11 1 -1.112800 0.733014 8.956180 7.270280 # O
32 11 2 0.556400 0.723334 8.457920 8.118450 # H
33 11 2 0.556400 1.129240 8.333990 6.703650 # H
34 12 1 -1.112800 11.229600 5.419700 10.216400 # O
35 12 2 0.556400 11.257700 5.103210 9.245840 # H
36 12 2 0.556400 11.472200 4.626020 10.675700 # H
37 13 1 -1.112800 1.539670 4.958490 7.189480 # O
38 13 2 0.556400 1.878900 4.355830 7.898400 # H
39 13 2 0.556400 0.608435 4.871290 7.333760 # H
40 14 1 -1.112800 5.194700 12.585900 11.877400 # O
41 14 2 0.556400 4.461940 12.002400 11.789800 # H
42 14 2 0.556400 5.800990 12.245600 12.546000 # H
43 15 1 -1.112800 10.541200 2.760930 3.671840 # O
44 15 2 0.556400 11.379900 3.110720 3.527720 # H
45 15 2 0.556400 10.563000 2.456660 4.545780 # H
46 16 1 -1.112800 1.735430 7.179310 5.391120 # O
47 16 2 0.556400 1.912490 6.544840 6.054940 # H
48 16 2 0.556400 0.898627 6.824870 5.088220 # H
49 17 1 -1.112800 6.877010 9.701870 4.336910 # O
50 17 2 0.556400 7.706420 9.450460 3.962120 # H
51 17 2 0.556400 6.830650 10.663800 4.252280 # H
52 18 1 -1.112800 8.923860 10.150500 7.400990 # O
53 18 2 0.556400 9.602800 9.557930 7.035830 # H
54 18 2 0.556400 8.369470 9.565990 7.937380 # H
55 19 1 -1.112800 10.783800 1.901810 6.155600 # O
56 19 2 0.556400 10.112100 1.498190 6.720110 # H
57 19 2 0.556400 11.535100 1.720670 6.693580 # H
58 20 1 -1.112800 5.227830 4.006860 2.302480 # O
59 20 2 0.556400 6.032370 4.085210 2.819820 # H
60 20 2 0.556400 5.290180 3.534110 1.481430 # H
61 21 1 -1.112800 5.125500 6.303080 8.382970 # O
62 21 2 0.556400 5.806420 5.617560 8.363370 # H
63 21 2 0.556400 4.490420 6.026330 7.778310 # H
64 22 1 -1.112800 0.456225 1.612050 8.056750 # O
65 22 2 0.556400 -0.025900 1.631960 8.898430 # H
66 22 2 0.556400 0.669755 0.625552 7.930950 # H
67 23 1 -1.112800 8.782040 3.471990 0.076822 # O
68 23 2 0.556400 8.202080 3.783770 0.746958 # H
69 23 2 0.556400 8.289680 3.164470 -0.665500 # H
70 24 1 -1.112800 1.672550 11.525400 7.292890 # O
71 24 2 0.556400 2.516940 11.757200 7.647260 # H
72 24 2 0.556400 1.487570 10.628700 7.531310 # H
73 25 1 -1.112800 1.364380 1.590440 3.663260 # O
74 25 2 0.556400 1.547320 1.223950 2.810090 # H
75 25 2 0.556400 1.074800 0.873519 4.174980 # H
76 26 1 -1.112800 8.689780 0.747241 7.379040 # O
77 26 2 0.556400 8.349180 0.921581 8.253930 # H
78 26 2 0.556400 9.036230 -0.154800 7.321810 # H
79 27 1 -1.112800 4.073020 8.755140 6.871380 # O
80 27 2 0.556400 4.306480 9.677620 6.980050 # H
81 27 2 0.556400 3.814440 8.535430 7.766820 # H
82 28 1 -1.112800 0.498442 3.851310 2.444790 # O
83 28 2 0.556400 0.654284 3.038590 2.870310 # H
84 28 2 0.556400 1.085810 4.484760 2.771370 # H
85 29 1 -1.112800 1.632160 11.104300 4.639990 # O
86 29 2 0.556400 1.743950 11.223400 5.572490 # H
87 29 2 0.556400 0.716740 10.800100 4.534040 # H
88 30 1 -1.112800 11.501400 1.217000 10.514400 # O
89 30 2 0.556400 10.582200 0.941987 10.575700 # H
90 30 2 0.556400 11.606600 1.981940 11.138600 # H
91 31 1 -1.112800 7.555960 0.146718 1.260860 # O
92 31 2 0.556400 7.949870 -0.667300 1.043520 # H
93 31 2 0.556400 7.138220 -0.047500 2.115990 # H
94 32 1 -1.112800 6.878570 7.721550 6.541450 # O
95 32 2 0.556400 7.135770 8.376320 5.940780 # H
96 32 2 0.556400 5.970910 7.920750 6.721600 # H
97 33 1 -1.112800 7.982210 5.292580 6.003760 # O
98 33 2 0.556400 8.909520 5.411240 5.926560 # H
99 33 2 0.556400 7.652470 6.207230 6.044110 # H
100 34 1 -1.112800 5.616110 10.935500 6.811260 # O
101 34 2 0.556400 6.363500 10.479300 6.482600 # H
102 34 2 0.556400 5.919440 11.184400 7.657440 # H
103 35 1 -1.112800 1.790630 0.357214 1.054180 # O
104 35 2 0.556400 1.057720 -0.216500 0.738618 # H
105 35 2 0.556400 1.953810 1.002820 0.368886 # H
106 36 1 -1.112800 10.283000 6.567040 2.571750 # O
107 36 2 0.556400 9.663420 6.322490 1.952700 # H
108 36 2 0.556400 11.030100 6.486050 1.980270 # H
109 37 1 -1.112800 2.290660 2.508490 11.784300 # O
110 37 2 0.556400 2.307070 2.658020 10.827900 # H
111 37 2 0.556400 2.081570 3.326220 12.203200 # H
112 38 1 -1.112800 7.227130 2.546230 10.396400 # O
113 38 2 0.556400 6.387210 2.711920 10.860900 # H
114 38 2 0.556400 7.452090 3.339380 9.859950 # H
115 39 1 -1.112800 10.713300 8.703520 6.190950 # O
116 39 2 0.556400 10.819800 9.249690 5.391950 # H
117 39 2 0.556400 11.524100 8.799950 6.668930 # H
118 40 1 -1.112800 12.000900 11.351800 0.188623 # O
119 40 2 0.556400 11.848900 11.826300 -0.697100 # H
120 40 2 0.556400 11.560000 11.967800 0.744819 # H
121 41 1 -1.112800 7.613350 4.878920 8.986350 # O
122 41 2 0.556400 7.858040 5.206450 8.126690 # H
123 41 2 0.556400 8.153130 5.431090 9.580010 # H
124 42 1 -1.112800 9.399660 9.104240 3.193160 # O
125 42 2 0.556400 9.192160 9.329720 2.265890 # H
126 42 2 0.556400 9.746630 8.194570 3.038160 # H
127 43 1 -1.112800 6.110810 12.293200 9.256280 # O
128 43 2 0.556400 5.674220 12.030500 10.043000 # H
129 43 2 0.556400 6.211290 13.269039 9.193900 # H
130 44 1 -1.112800 8.977380 0.134346 10.851900 # O
131 44 2 0.556400 8.406550 -0.509500 10.478500 # H
132 44 2 0.556400 8.472070 0.738628 11.418100 # H
133 45 1 -1.112800 10.737500 6.125960 5.402620 # O
134 45 2 0.556400 10.814800 7.033850 5.668770 # H
135 45 2 0.556400 10.473200 5.989030 4.507260 # H
136 46 1 -1.112800 2.828860 5.338020 3.155120 # O
137 46 2 0.556400 3.115240 6.111620 3.566130 # H
138 46 2 0.556400 3.652960 4.901350 2.802110 # H
139 47 1 -1.112800 11.623100 8.822650 11.443800 # O
140 47 2 0.556400 11.819000 8.028750 11.942900 # H
141 47 2 0.556400 11.846900 9.639150 11.910200 # H
142 48 1 -1.112800 2.196920 5.192020 0.491763 # O
143 48 2 0.556400 2.397930 5.229040 1.410490 # H
144 48 2 0.556400 2.944260 5.694820 0.162800 # H
145 49 1 -1.112800 3.293400 9.113640 1.147790 # O
146 49 2 0.556400 3.487550 9.977400 1.432320 # H
147 49 2 0.556400 2.748220 8.848930 1.907350 # H
148 50 1 -1.112800 11.088800 11.001400 4.049660 # O
149 50 2 0.556400 10.878300 11.717500 3.452910 # H
150 50 2 0.556400 10.463700 10.416800 3.674780 # H
151 51 1 -1.112800 3.297820 10.609800 11.272100 # O
152 51 2 0.556400 2.695600 10.181300 11.864000 # H
153 51 2 0.556400 3.766060 9.889320 10.814000 # H
154 52 1 -1.112800 5.136170 2.839760 12.047300 # O
155 52 2 0.556400 4.182540 2.709670 11.986300 # H
156 52 2 0.556400 5.277560 1.871320 12.145200 # H
157 53 1 -1.112800 6.666230 9.750290 11.852900 # O
158 53 2 0.556400 6.315340 8.898120 12.198600 # H
159 53 2 0.556400 6.880880 9.588630 10.927400 # H
160 54 1 -1.112800 7.880750 4.211900 3.434410 # O
161 54 2 0.556400 7.759280 4.346270 4.378860 # H
162 54 2 0.556400 8.768200 3.904830 3.353740 # H
163 55 1 -1.112800 7.546130 8.662960 9.307760 # O
164 55 2 0.556400 7.028650 8.213840 8.622330 # H
165 55 2 0.556400 8.051960 7.927860 9.666640 # H
166 56 1 -1.112800 0.717537 7.543310 9.627180 # O
167 56 2 0.556400 0.228081 8.210400 10.105500 # H
168 56 2 0.556400 0.266932 6.740440 9.750090 # H
169 57 1 -1.112800 10.591100 0.623171 1.865850 # O
170 57 2 0.556400 10.652000 1.452080 2.386840 # H
171 57 2 0.556400 9.783430 0.698423 1.363370 # H
172 58 1 -1.112800 7.938210 5.958010 1.384490 # O
173 58 2 0.556400 7.761390 5.536490 2.192400 # H
174 58 2 0.556400 7.064090 6.249180 1.117290 # H
175 59 1 -1.112800 4.821800 3.105970 7.521330 # O
176 59 2 0.556400 5.280230 2.334520 7.062320 # H
177 59 2 0.556400 4.472030 3.743860 6.875430 # H
178 60 1 -1.112800 4.496900 8.048400 4.270050 # O
179 60 2 0.556400 3.940060 8.538270 4.870210 # H
180 60 2 0.556400 5.255640 8.647290 4.082050 # H
181 61 1 -1.112800 11.300500 4.664560 7.618120 # O
182 61 2 0.556400 11.339900 3.754300 7.379660 # H
183 61 2 0.556400 11.049300 5.095730 6.782970 # H
184 62 1 -1.112800 11.510900 3.596380 12.157800 # O
185 62 2 0.556400 12.128900 3.876530 12.911516 # H
186 62 2 0.556400 10.542300 3.585180 12.332377 # H
187 63 1 -1.112800 2.566340 3.003840 9.021310 # O
188 63 2 0.556400 3.424460 2.785510 8.628220 # H
189 63 2 0.556400 1.892970 2.412700 8.700380 # H
190 64 1 -1.112800 3.356960 8.132790 9.544550 # O
191 64 2 0.556400 2.459540 7.801110 9.736580 # H
192 64 2 0.556400 3.866730 7.387220 9.753740 # H
Bonds
1 1 1 2
2 1 1 3
3 1 4 5
4 1 4 6
5 1 7 8
6 1 7 9
7 1 10 11
8 1 10 12
9 1 13 14
10 1 13 15
11 1 16 17
12 1 16 18
13 1 19 20
14 1 19 21
15 1 22 23
16 1 22 24
17 1 25 26
18 1 25 27
19 1 28 29
20 1 28 30
21 1 31 32
22 1 31 33
23 1 34 35
24 1 34 36
25 1 37 38
26 1 37 39
27 1 40 41
28 1 40 42
29 1 43 44
30 1 43 45
31 1 46 47
32 1 46 48
33 1 49 50
34 1 49 51
35 1 52 53
36 1 52 54
37 1 55 56
38 1 55 57
39 1 58 59
40 1 58 60
41 1 61 62
42 1 61 63
43 1 64 65
44 1 64 66
45 1 67 68
46 1 67 69
47 1 70 71
48 1 70 72
49 1 73 74
50 1 73 75
51 1 76 77
52 1 76 78
53 1 79 80
54 1 79 81
55 1 82 83
56 1 82 84
57 1 85 86
58 1 85 87
59 1 88 89
60 1 88 90
61 1 91 92
62 1 91 93
63 1 94 95
64 1 94 96
65 1 97 98
66 1 97 99
67 1 100 101
68 1 100 102
69 1 103 104
70 1 103 105
71 1 106 107
72 1 106 108
73 1 109 110
74 1 109 111
75 1 112 113
76 1 112 114
77 1 115 116
78 1 115 117
79 1 118 119
80 1 118 120
81 1 121 122
82 1 121 123
83 1 124 125
84 1 124 126
85 1 127 128
86 1 127 129
87 1 130 131
88 1 130 132
89 1 133 134
90 1 133 135
91 1 136 137
92 1 136 138
93 1 139 140
94 1 139 141
95 1 142 143
96 1 142 144
97 1 145 146
98 1 145 147
99 1 148 149
100 1 148 150
101 1 151 152
102 1 151 153
103 1 154 155
104 1 154 156
105 1 157 158
106 1 157 159
107 1 160 161
108 1 160 162
109 1 163 164
110 1 163 165
111 1 166 167
112 1 166 168
113 1 169 170
114 1 169 171
115 1 172 173
116 1 172 174
117 1 175 176
118 1 175 177
119 1 178 179
120 1 178 180
121 1 181 182
122 1 181 183
123 1 184 185
124 1 184 186
125 1 187 188
126 1 187 189
127 1 190 191
128 1 190 192
Angles
1 1 2 1 3
2 1 5 4 6
3 1 8 7 9
4 1 11 10 12
5 1 14 13 15
6 1 17 16 18
7 1 20 19 21
8 1 23 22 24
9 1 26 25 27
10 1 29 28 30
11 1 32 31 33
12 1 35 34 36
13 1 38 37 39
14 1 41 40 42
15 1 44 43 45
16 1 47 46 48
17 1 50 49 51
18 1 53 52 54
19 1 56 55 57
20 1 59 58 60
21 1 62 61 63
22 1 65 64 66
23 1 68 67 69
24 1 71 70 72
25 1 74 73 75
26 1 77 76 78
27 1 80 79 81
28 1 83 82 84
29 1 86 85 87
30 1 89 88 90
31 1 92 91 93
32 1 95 94 96
33 1 98 97 99
34 1 101 100 102
35 1 104 103 105
36 1 107 106 108
37 1 110 109 111
38 1 113 112 114
39 1 116 115 117
40 1 119 118 120
41 1 122 121 123
42 1 125 124 126
43 1 128 127 129
44 1 131 130 132
45 1 134 133 135
46 1 137 136 138
47 1 140 139 141
48 1 143 142 144
49 1 146 145 147
50 1 149 148 150
51 1 152 151 153
52 1 155 154 156
53 1 158 157 159
54 1 161 160 162
55 1 164 163 165
56 1 167 166 168
57 1 170 169 171
58 1 173 172 174
59 1 176 175 177
60 1 179 178 180
61 1 182 181 183
62 1 185 184 186
63 1 188 187 189
64 1 191 190 192

40
examples/PACKAGES/gle/in.h2o-quantum Normal file
View File

@ -0,0 +1,40 @@
units real
atom_style full
pair_style lj/cut/tip4p/long 1 2 1 1 0.14714951 8
bond_style class2
angle_style harmonic
kspace_style pppm/tip4p 0.0001
read_data data.h2o-quantum
pair_coeff * 2 0.0 0.0
pair_coeff 1 1 0.1852 3.1589022
#q-tip4pf bond parameters
bond_coeff 1 0.9419 607.19354 -1388.6516 1852.577
angle_coeff 1 43.93 107.4
timestep 0.5
# mean velocity is higher than target T because of zero point energy
velocity all create 800.0 1112 dist gaussian mom yes
thermo 100
thermo_style custom step temp pe ke etotal
# some problem
fix 1 all gle 6 300.0 300.0 31415 qt-300k.A noneq qt-300k.C
#dump 1 all atom 100 h2o-smart.lammpstrj
#dump 2 all image 1000 h2o-smart.*.jpg element element &
# zoom 1.4
#dump_modify 2 pad 5 element O H
#dump 3 all movie 100 movie.mp4 element element &
# zoom 1.4
#dump_modify 3 pad 5 element O H
run 10000

40
examples/PACKAGES/gle/in.h2o-smart Normal file
View File

@ -0,0 +1,40 @@
units real
atom_style full
pair_style lj/cut/tip4p/long 1 2 1 1 0.14714951 8
bond_style class2
angle_style harmonic
kspace_style pppm/tip4p 0.0001
read_data data.h2o-smart
pair_coeff * 2 0.0 0.0
pair_coeff 1 1 0.1852 3.1589022
#q-tip4pf bond parameters
bond_coeff 1 0.9419 607.19354 -1388.6516 1852.577
angle_coeff 1 43.93 107.4
timestep 0.5
velocity all create 300.0 1112 dist gaussian mom yes
thermo 100
thermo_style custom step temp pe ke etotal
# smart sampling with GLE: best efficiency on slow diffusive modes,
# and as good as possible on higher-frequency modes
fix 1 all gle 6 300.0 300.0 31415 smart.A
#dump 1 all atom 100 h2o-smart.lammpstrj
#dump 2 all image 1000 h2o-smart.*.jpg element element &
# zoom 1.4
#dump_modify 2 pad 5 element O H
#dump 3 all movie 100 movie.mp4 element element &
# zoom 1.4
#dump_modify 3 pad 5 element O H
run 10000

201
examples/PACKAGES/gle/log.h2o-quantum Normal file
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@ -0,0 +1,201 @@
LAMMPS (1 Aug 2014-ICMS)
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:79)
using 1 OpenMP thread(s) per MPI task
units real
atom_style full
pair_style lj/cut/tip4p/long 1 2 1 1 0.14714951 8
bond_style class2
angle_style harmonic
kspace_style pppm/tip4p 0.0001
read_data data.h2o-quantum
orthogonal box = (-0.025952 -0.072222 0.103767) to (12.3984 12.3522 12.5282)
1 by 1 by 2 MPI processor grid
reading atoms ...
192 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
128 bonds
reading angles ...
64 angles
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
pair_coeff * 2 0.0 0.0
pair_coeff 1 1 0.1852 3.1589022
#q-tip4pf bond parameters
bond_coeff 1 0.9419 607.19354 -1388.6516 1852.577
angle_coeff 1 43.93 107.4
timestep 0.5
# mean velocity is higher than target T because of zero point energy
velocity all create 800.0 1112 dist gaussian mom yes
thermo 100
thermo_style custom step temp pe ke etotal
# some problem
fix 1 all gle 6 300.0 300.0 31415 qt-300k.A noneq qt-300k.C
Reading A-matrix from qt-300k.A
Reading C-matrix from qt-300k.C
fix_modify 1 energy no
#dump 1 all atom 100 h2o-smart.lammpstrj
#dump 2 all image 1000 h2o-smart.*.jpg element element # zoom 1.4
#dump_modify 2 pad 5 element O H
#dump 3 all movie 100 movie.mp4 element element # zoom 1.4
#dump_modify 3 pad 5 element O H
run 10000
PPPM initialization ...
extracting TIP4P info from Pair style
G vector (1/distance) = 0.352417
grid = 10 10 10
stencil order = 5
estimated absolute RMS force accuracy = 0.0229722
estimated relative force accuracy = 6.91802e-05
using double precision FFTs
3d grid and FFT values/proc = 3468 500
Memory usage per processor = 13.8311 Mbytes
Step Temp PotEng KinEng TotEng
0 800 -397.88979 455.46778 57.577983
100 698.89108 -392.66653 397.90296 5.2364322
200 688.37522 -392.58656 391.91592 -0.67064832
300 643.34468 -419.2295 366.27846 -52.95104
400 660.33491 -418.20153 375.95159 -42.249944
500 680.44413 -388.82235 387.40047 -1.421883
600 742.26981 -421.13842 422.59997 1.4615499
700 749.05719 -385.72409 426.46427 40.740176
800 718.09546 -364.1074 408.83668 44.729275
900 753.71034 -384.48404 429.11347 44.629426
1000 726.27048 -368.42604 413.491 45.064959
1100 671.85382 -388.36627 382.50971 -5.856561
1200 766.4481 -435.01383 436.36551 1.3516866
1300 723.91972 -395.01705 412.15263 17.135583
1400 803.73405 -386.55381 457.5937 71.039894
1500 800.56883 -362.15289 455.79163 93.638742
1600 792.51193 -351.50213 451.20456 99.702431
1700 806.09904 -368.494 458.94017 90.446168
1800 785.11513 -386.8046 446.9933 60.188709
1900 793.18902 -367.16729 451.59005 84.422754
2000 849.13258 -376.69692 483.44066 106.74374
2100 772.95581 -334.17532 440.07058 105.89526
2200 758.55925 -345.91518 431.87412 85.958942
2300 795.84944 -362.23959 453.10472 90.86513
2400 796.99718 -338.15171 453.75817 115.60646
2500 874.90618 -405.30041 498.11446 92.814051
2600 812.20702 -345.27738 462.41766 117.14027
2700 756.661 -373.04782 430.79338 57.745555
2800 689.49938 -351.84148 392.55594 40.714461
2900 703.97902 -363.39946 400.7997 37.400241
3000 682.07274 -375.9771 388.32769 12.350595
3100 720.56258 -379.09322 410.24129 31.14807
3200 869.51663 -429.58952 495.04601 65.456488
3300 778.68875 -395.97562 443.33454 47.358919
3400 704.36128 -348.83409 401.01733 52.183237
3500 735.73637 -435.36664 418.88026 -16.486378
3600 755.04937 -432.78096 429.87582 -2.9051363
3700 637.56555 -380.38446 362.9882 -17.396255
3800 767.44468 -434.86704 436.9329 2.0658581
3900 747.21672 -450.05408 425.41642 -24.637657
4000 641.85869 -399.2507 365.43244 -33.818259
4100 715.57343 -464.53214 407.4008 -57.131338
4200 687.53534 -428.6068 391.43774 -37.16906
4300 736.74705 -410.46396 419.45568 8.9917162
4400 708.2022 -413.96687 403.2041 -10.762766
4500 718.23813 -416.4572 408.91791 -7.5392908
4600 660.42739 -409.18265 376.00424 -33.178411
4700 683.154 -397.11041 388.94329 -8.1671176
4800 736.51784 -389.65074 419.32518 29.674437
4900 682.52561 -357.82169 388.58553 30.763836
5000 724.71854 -376.94756 412.60742 35.659862
5100 787.80577 -380.82211 448.52518 67.703069
5200 849.22392 -387.60456 483.49266 95.888099
5300 785.66154 -373.38849 447.30439 73.915905
5400 836.11588 -418.91104 476.0298 57.118761
5500 749.52387 -389.88805 426.72996 36.841907
5600 743.71711 -395.52608 423.42397 27.897893
5700 786.54536 -422.76435 447.80758 25.043234
5800 736.12533 -398.40046 419.10171 20.701243
5900 679.07763 -370.47116 386.62247 16.151313
6000 646.63246 -390.0465 368.15031 -21.896187
6100 667.52401 -375.38048 380.0446 4.6641215
6200 662.0449 -356.05116 376.92515 20.873991
6300 722.24271 -389.25064 411.19785 21.947208
6400 741.74425 -403.61369 422.30075 18.687067
6500 744.81344 -334.39156 424.04815 89.656589
6600 703.33813 -302.17937 400.43482 98.255449
6700 762.72179 -315.74663 434.244 118.49737
6800 777.14808 -358.53951 442.45738 83.917874
6900 740.91016 -341.14608 421.82588 80.679798
7000 813.65774 -349.90677 463.2436 113.33683
7100 776.23657 -358.76727 441.93843 83.171162
7200 749.14904 -377.5127 426.51656 49.003859
7300 813.83914 -371.97142 463.34688 91.375458
7400 784.40735 -373.09126 446.59034 73.499082
7500 756.56416 -308.48261 430.73824 122.25563
7600 843.78231 -366.02787 480.39456 114.36669
7700 812.6389 -376.78072 462.66354 85.882816
7800 891.73869 -374.24914 507.6978 133.44866
7900 832.91822 -310.07315 474.20926 164.1361
8000 792.50793 -286.32992 451.20228 164.87237
8100 816.61062 -314.92959 464.92478 149.99518
8200 767.57709 -277.06101 437.00829 159.94727
8300 820.33206 -313.40163 467.04353 153.6419
8400 846.28718 -373.60278 481.82067 108.2179
8500 792.15839 -364.19518 451.00327 86.808099
8600 763.69922 -373.27473 434.80048 61.525753
8700 787.21065 -374.09876 448.18635 74.08759
8800 771.3359 -372.99149 439.14831 66.156816
8900 751.28308 -387.66958 427.73154 40.061962
9000 766.47003 -417.13174 436.378 19.246259
9100 664.37523 -361.53151 378.25189 16.720375
9200 797.99252 -413.81272 454.32485 40.512127
9300 749.56217 -407.82336 426.75177 18.928408
9400 727.96573 -392.49341 414.45617 21.962757
9500 731.99963 -403.99536 416.75281 12.757445
9600 719.48179 -398.62338 409.62596 11.002579
9700 726.60611 -387.18124 413.68209 26.500847
9800 685.69606 -386.79227 390.39057 3.5983035
9900 725.5619 -419.90553 413.08758 -6.8179505
10000 658.44792 -383.61406 374.87726 -8.7367979
Loop time of 11.7068 on 2 procs for 10000 steps with 192 atoms
96.5% CPU use with 2 MPI tasks x 1 OpenMP threads
Performance: 36.902 ns/day 0.650 hours/ns 854.202 timesteps/s
MPI task timings breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.7083 | 6.1014 | 6.4946 | 15.9 | 52.12
Bond | 0.044239 | 0.048708 | 0.053176 | 2.0 | 0.42
Kspace | 1.628 | 2.0108 | 2.3937 | 27.0 | 17.18
Neigh | 0.082288 | 0.082289 | 0.082291 | 0.0 | 0.70
Comm | 0.52311 | 0.54494 | 0.56677 | 3.0 | 4.65
Output | 0.0027063 | 0.0029016 | 0.0030968 | 0.4 | 0.02
Modify | 2.6603 | 2.7619 | 2.8636 | 6.1 | 23.59
Other | | 0.1538 | | | 1.31
Nlocal: 96 ave 97 max 95 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 2802.5 ave 2823 max 2782 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 21984.5 ave 22586 max 21383 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 43969
Ave neighs/atom = 229.005
Ave special neighs/atom = 2
Neighbor list builds = 102
Dangerous builds = 0

200
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LAMMPS (1 Aug 2014-ICMS)
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:79)
using 1 OpenMP thread(s) per MPI task
units real
atom_style full
pair_style lj/cut/tip4p/long 1 2 1 1 0.14714951 8
bond_style class2
angle_style harmonic
kspace_style pppm/tip4p 0.0001
read_data data.h2o-smart
orthogonal box = (-0.1607 0.08867 -0.104992) to (12.2637 12.5131 12.3194)
1 by 1 by 2 MPI processor grid
reading atoms ...
192 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
128 bonds
reading angles ...
64 angles
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
pair_coeff * 2 0.0 0.0
pair_coeff 1 1 0.1852 3.1589022
#q-tip4pf bond parameters
bond_coeff 1 0.9419 607.19354 -1388.6516 1852.577
angle_coeff 1 43.93 107.4
timestep 0.5
velocity all create 300.0 1112 dist gaussian mom yes
thermo 100
thermo_style custom step temp pe ke etotal
# smart sampling with GLE: best efficiency on slow diffusive modes,
# and as good as possible on higher-frequency modes
fix 1 all gle 6 300.0 300.0 31415 smart.A
Reading A-matrix from smart.A
fix_modify 1 energy no
#dump 1 all atom 100 h2o-smart.lammpstrj
#dump 2 all image 1000 h2o-smart.*.jpg element element # zoom 1.4
#dump_modify 2 pad 5 element O H
#dump 3 all movie 100 movie.mp4 element element # zoom 1.4
#dump_modify 3 pad 5 element O H
run 10000
PPPM initialization ...
extracting TIP4P info from Pair style
G vector (1/distance) = 0.352417
grid = 10 10 10
stencil order = 5
estimated absolute RMS force accuracy = 0.0229722
estimated relative force accuracy = 6.91802e-05
using double precision FFTs
3d grid and FFT values/proc = 3468 500
Memory usage per processor = 13.829 Mbytes
Step Temp PotEng KinEng TotEng
0 300 -670.21264 170.80042 -499.41223
100 290.62622 -664.95618 165.4636 -499.49258
200 297.41006 -668.85033 169.32587 -499.52445
300 305.07683 -670.08926 173.69083 -496.39843
400 297.11048 -660.75391 169.15531 -491.5986
500 307.19396 -671.82767 174.89619 -496.93149
600 268.36604 -656.32235 152.7901 -503.53225
700 271.3451 -658.6792 154.48619 -504.19302
800 283.6159 -654.86696 161.47238 -493.39458
900 295.4066 -655.55317 168.18523 -487.36794
1000 325.36725 -671.99548 185.24287 -486.75261
1100 307.57921 -661.18796 175.11553 -486.07244
1200 294.09368 -663.56195 167.43774 -496.12421
1300 284.1081 -658.9576 161.75261 -497.20499
1400 297.09449 -672.08 169.14621 -502.93379
1500 294.08366 -667.83813 167.43204 -500.40609
1600 283.41095 -658.69002 161.35569 -497.33433
1700 266.72675 -652.17689 151.8568 -500.32009
1800 284.11152 -665.90232 161.75455 -504.14777
1900 295.00703 -669.07696 167.95775 -501.11921
2000 286.16635 -664.63252 162.92444 -501.70809
2100 283.09707 -664.82636 161.17699 -503.64936
2200 282.1225 -667.27283 160.62213 -506.6507
2300 278.48023 -667.54864 158.54846 -509.00017
2400 283.68359 -666.02167 161.51092 -504.51076
2500 285.0694 -657.94904 162.29991 -495.64913
2600 282.1023 -655.28463 160.61063 -494.674
2700 294.69375 -651.3296 167.77938 -483.55021
2800 296.53348 -657.16696 168.82681 -488.34015
2900 288.72568 -658.98174 164.38155 -494.60019
3000 291.30593 -661.20218 165.85058 -495.3516
3100 294.56923 -658.71954 167.70849 -491.01105
3200 287.91872 -657.09451 163.92212 -493.17239
3300 315.70884 -658.37955 179.744 -478.63554
3400 300.70872 -647.40117 171.20391 -476.19725
3500 317.80728 -644.59007 180.93872 -463.65135
3600 293.42867 -626.24901 167.05913 -459.18988
3700 294.04489 -632.36234 167.40997 -464.95237
3800 313.99457 -642.62858 178.76801 -463.86058
3900 321.96877 -643.18611 183.308 -459.87811
4000 307.80414 -638.51198 175.24358 -463.26839
4100 306.46742 -631.99291 174.48254 -457.51037
4200 297.95493 -625.59735 169.63609 -455.96127
4300 311.77725 -629.02415 177.50561 -451.51854
4400 321.12007 -639.20414 182.8248 -456.37934
4500 305.83311 -639.85511 174.12141 -465.7337
4600 280.0309 -626.77621 159.43131 -467.34489
4700 299.91194 -646.01678 170.75028 -475.26649
4800 314.30179 -655.43971 178.94292 -476.49679
4900 296.41005 -648.52791 168.75653 -479.77138
5000 317.18225 -664.63778 180.58287 -484.05491
5100 297.61918 -653.87882 169.44493 -484.43389
5200 301.09579 -656.31563 171.42429 -484.89135
5300 276.84259 -632.08437 157.6161 -474.46827
5400 284.49059 -633.16522 161.97037 -471.19485
5500 304.31022 -638.47695 173.25437 -465.22257
5600 305.31764 -644.82828 173.82793 -471.00035
5700 299.58268 -655.88335 170.56282 -485.32053
5800 321.96167 -659.01664 183.30396 -475.71269
5900 316.28141 -660.23207 180.06999 -480.16208
6000 309.56412 -660.55788 176.2456 -484.31228
6100 330.02958 -678.57146 187.8973 -490.67417
6200 303.74539 -661.04985 172.93279 -488.11706
6300 307.74734 -658.31899 175.21125 -483.10774
6400 286.18649 -643.75179 162.93591 -480.81588
6500 289.44456 -649.15249 164.79084 -484.36165
6600 298.55754 -647.04558 169.97917 -477.0664
6700 283.95805 -655.73195 161.66717 -494.06477
6800 280.42279 -653.63036 159.65443 -493.97593
6900 271.83117 -649.79819 154.76292 -495.03527
7000 280.45299 -654.38347 159.67162 -494.71185
7100 296.81787 -653.83396 168.98872 -484.84524
7200 290.67067 -645.72083 165.4889 -480.23193
7300 295.56828 -663.74576 168.27729 -495.46847
7400 291.53853 -666.33819 165.98301 -500.35518
7500 279.92515 -654.38809 159.37111 -495.01698
7600 257.38847 -642.65325 146.54019 -496.11306
7700 277.50516 -653.66423 157.99332 -495.6709
7800 311.52678 -672.32432 177.36301 -494.9613
7900 298.23749 -660.82827 169.79696 -491.03131
8000 307.29237 -666.78322 174.95222 -491.831
8100 313.63507 -663.57608 178.56333 -485.01274
8200 296.97756 -664.0781 169.07964 -494.99846
8300 296.67648 -675.06782 168.90822 -506.1596
8400 285.95501 -670.79975 162.80411 -507.99564
8500 283.47207 -667.97661 161.39049 -506.58612
8600 269.45464 -660.64217 153.40988 -507.23229
8700 260.20768 -662.98385 148.14527 -514.83858
8800 291.86372 -679.90597 166.16815 -513.73782
8900 300.0625 -680.41871 170.836 -509.58271
9000 310.75541 -677.23429 176.92384 -500.31045
9100 290.3936 -663.51571 165.33116 -498.18455
9200 335.88148 -681.97626 191.22899 -490.74727
9300 274.72824 -648.88125 156.41233 -492.46892
9400 266.86084 -644.89957 151.93314 -492.96643
9500 282.71448 -658.10319 160.95917 -497.14402
9600 286.78087 -661.06015 163.2743 -497.78584
9700 280.54912 -648.27141 159.72635 -488.54506
9800 314.25211 -655.39099 178.91464 -476.47636
9900 306.26043 -643.12511 174.3647 -468.76042
10000 323.66711 -662.08608 184.27492 -477.81115
Loop time of 11.8044 on 2 procs for 10000 steps with 192 atoms
97.0% CPU use with 2 MPI tasks x 1 OpenMP threads
Performance: 36.596 ns/day 0.656 hours/ns 847.141 timesteps/s
MPI task timings breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.0343 | 6.2649 | 6.4955 | 9.2 | 53.07
Bond | 0.046165 | 0.048247 | 0.050328 | 0.9 | 0.41
Kspace | 1.7227 | 1.947 | 2.1712 | 16.1 | 16.49
Neigh | 0.094508 | 0.094514 | 0.09452 | 0.0 | 0.80
Comm | 0.52919 | 0.54233 | 0.55547 | 1.8 | 4.59
Output | 0.0018249 | 0.0028317 | 0.0038385 | 1.9 | 0.02
Modify | 2.7063 | 2.7612 | 2.8162 | 3.3 | 23.39
Other | | 0.1434 | | | 1.21
Nlocal: 96 ave 99 max 93 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 2799 ave 2832 max 2766 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 21917.5 ave 22938 max 20897 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 43835
Ave neighs/atom = 228.307
Ave special neighs/atom = 2
Neighbor list builds = 116
Dangerous builds = 0

7
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3.904138445158e-4 4.681059722010e-2 3.079778738058e-2 4.428079381336e-2 5.057825203477e-2 2.591193419597e-2 1.513907125942e-2
-4.789343294190e-2 2.037551040972e-2 6.597801861779e-2 -8.528273506602e-3 -2.230839572773e-3 6.593086307870e-3 -6.653653981891e-2
-2.905096373618e-2 -6.597801861779e-2 2.086885297843e-2 1.145471984072e-2 3.111465343867e-2 1.101562087523e-2 -3.264959166486e-2
-4.435072214164e-2 8.528273506602e-3 -1.145471984072e-2 2.386233403354e-2 8.792083035892e-4 2.994937741424e-2 1.530348823334e-2
-4.916924816292e-2 2.230839572773e-3 -3.111465343867e-2 -8.792083035892e-4 2.606519350778e-2 -3.458690409590e-2 9.744362519913e-2
-1.301834364438e-2 -6.593086307870e-3 -1.101562087523e-2 -2.994937741424e-2 3.458690409590e-2 2.365664840227e-1 -3.253589816948e-1
-3.003491620426e-2 6.653653981891e-2 3.264959166486e-2 -1.530348823334e-2 -9.744362519913e-2 3.253589816948e-1 3.833684611452e-1

7
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2.999985914100e+2 5.937593337000e+0 2.144376751500e+2 5.883055908000e+1 -1.119803766000e+2 -6.793381764000e+1 1.379789732400e+1
5.937593337000e+0 3.781851303000e+2 -5.794518522000e+1 -2.178772681500e+2 -1.649310659100e+2 -6.557113452000e+1 3.833830743000e+1
2.144376751500e+2 -5.794518522000e+1 7.325759985000e+2 2.188507713000e+2 -3.704586531000e+2 -3.385193865000e+1 -4.827706758000e+0
5.883055908000e+1 -2.178772681500e+2 2.188507713000e+2 6.960431520000e+2 -3.630171093000e+2 1.702940985000e+2 -6.073265904000e+1
-1.119803766000e+2 -1.649310659100e+2 -3.704586531000e+2 -3.630171093000e+2 1.437872295000e+3 1.124747403900e+2 3.533754279000e+0
-6.793381764000e+1 -6.557113452000e+1 -3.385193865000e+1 1.702940985000e+2 1.124747403900e+2 1.489339230300e+3 -1.607601813300e+2
1.379789732400e+1 3.833830743000e+1 -4.827706758000e+0 -6.073265904000e+1 3.533754279000e+0 -1.607601813300e+2 4.445083650000e+2

7
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4.247358737218e-3 3.231404593065e-2 -9.715629522215e-3 8.199488441225e-3 7.288427565896e-3 -3.634229949055e-3 -3.294395982200e-3
4.887738278128e-2 5.978602802893e-1 -2.079222967202e-1 1.088740438247e-1 4.666954324786e-2 -1.334147134493e-2 -3.914996645811e-2
4.015863091190e-2 2.079222967202e-1 1.645970119444e-1 8.351952991453e-2 5.114740085468e-2 1.217862237677e-2 -4.506711205974e-2
-7.988115185559e-3 -1.088740438247e-1 -8.351952991453e-2 4.726009106840e-4 3.048388792335e-2 -1.182268544760e-2 4.862010553750e-3
-7.287991634294e-3 -4.666954324786e-2 -5.114740085468e-2 -3.048388792335e-2 5.503167644558e-6 -1.852347991021e-2 1.430002486694e-2
3.630267324412e-3 1.334147134493e-2 -1.217862237677e-2 1.182268544760e-2 1.852347991021e-2 8.684650261894e-7 -3.576117734950e-3
3.294286772414e-3 3.914996645811e-2 4.506711205974e-2 -4.862010553750e-3 -1.430002486694e-2 3.576117734950e-3 2.821060581893e-9

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Generalized Replica Exchange Method (gREM) examples
===================================================
Examples:
---------------------------------------------------
lj-single:
This example is the simplest case scenario utilizing the generalized
ensemble defined by fix_grem. It utilizes only 1 replica and requires
the LAMMPS executable to be run as usual:
mpirun -np 4 lmp_mpi -in in.gREM-npt
./lmp_serial -in in.gREM-nvt
While this does not obtain any information about Ts(H), it is most similar to
a microcanonical simulation and "single-replica gREM" can be useful for
studying non-equilibrium processes as well.
lj-6rep:
This example utilizes an external python script to handle swaps between
replicas. Included is run.sh, which requires the path to your LAMMPS
executable. The python script is fragile as it relies on parsing output files
from the LAMMPS run and moving LAMMPS data files between directories. Use
caution if modifying this example further. If complied with mpi, multiple
processors can be used as:
./run.sh $NUM_PROCS
a serial run is completed simply as
./run.sh 1
where the executable provided must be serial if "1" is provided as the number
of procs. While this external replica exchange module is quite slow and
inefficient, it allows for many replicas to be used on a single processor.
While here there are only 6 replicas, this example could be extended to >100
replicas while still using a serial compilation. This is also beneficial for
running on high performance nodes with few cores to complete a full-scale gREM
simulation with a large number of replicas.
A quick note on efficiency: frequent exchanges slow down this script
substantially because LAMMPS is restarted every exchange attempt. The script
works best for large systems with infrequent exchanges.
lj-temper:
This is an example using the internal replica exchange module. While fast
in comparison to the python version, it requires substantial resources
(at least 1 proc per replica). Instead of stopping LAMMPS every exchange
attempt, all replicas are run concurrently, and exchanges take place
internally. This requires use of LAMMPS partition mode, via the command
line using the -p flag. Input files require world type variables defining
the parameters of each replica. The included example with 4 replicas must
run on at least 4 procs, in that case LAMMPS could be initiated as:
mpirun -np 4 lmp_mpi -p 4x1 -in in.gREM-temper
spawning 4 partitions with 1 replica each. Multiple procs per replica could
be used. In the case of a 16 system with 4 replicas, the
following logic could be used:
mpirun -np 16 lmp_mpi -p 4x4 -in in.gREM-temper
Once started, a universe log file will be created as well as log files for
each replica. The universe (log.lammps) contains exchange information, while
the replicas (*/log.lammps.*) contains the thermo_output as usual. In this
example, in.gREM-temper moves the log files to their respective folders.
Closing Notes:
---------------------------------------------------
Of significant difference between lj-6rep and lj-temper is the format of data.
In lj-6rep, data is stored as 'replicas' meaning discontinuous trajectories, as
files are moved between directories labeled by the 'lambda' of the replica. In
lj-temper, data is stored as 'walkers' with continuous trajectories, but
discontinuous parameters. The later is significantly more efficient, but
requires post-processing to obtain per-replica information.
Any problems/questions should be directed to <dstelter@bu.edu>.

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examples/PACKAGES/grem/lj-6rep/clean.sh Executable file
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#/bin/bash
for i in $(ls -d [0-9]*)
do
rm -f $i/final*
rm -f $i/log*
rm -f $i/ent*
rm -f $i/output
cp $i/restart.init $i/restart_file
done
echo 1 > lastexchange
cp walker.bkp lastwalker
exit 0

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#!/usr/bin/env python2.7
import os, sys
from numpy import *
import numpy.random
### Runs replica exchange with gREM (fix grem) for unlimited number of replicas on a set number of processors. This script is inefficient, but necessary if wanting to run with hundreds of replicas on relatively few number of procs.
### read number of processors from the command line
nproc = int(sys.argv[1])
### path to simulation directory
path = os.getcwd()
### path to LAMMPS executable
lmp = sys.argv[2]
### LAMMPS input name
inp = sys.argv[3]
### define pressure for simulations (0 if const V)
pressure = 0
### some constants for gREM, must match with LAMMPS input file!
H = -30000
eta = -0.01
#kB = 0.000086173324 # eV (metal)
kB = 0.0019872 # kcal/mol (real)
### define lambdas - script assumes that there are already existing directories with all files necessary to run
lambdas=[400,405,410,415,420,425]
ll = len(lambdas)
### define number of exchanges
starting_ex = int(loadtxt("lastexchange"))
how_many_ex = 5
max_exchange = starting_ex+how_many_ex
### array with walkers
walker = loadtxt("lastwalker")
### initiate array with enthalpies
enthalpy = zeros(ll)
aver_enthalpy = zeros(ll)
for exchange in arange(starting_ex,max_exchange):
print "run", exchange
for l in range(ll):
#print "replica", l
os.chdir(path+"/%s" % lambdas[l])
#os.system("cp restart_file restart_file%d" % exchange)
if (nproc > 1):
os.system("mpirun -np %d " % (nproc) + lmp + " -in ../" + inp + " -var lambda %g -var eta %g -var enthalpy %g > output" % (lambdas[l], eta, H))
if (nproc == 1):
os.system(lmp + " -in ../" + inp + " -var lambda %g -var eta %g -var enthalpy %g > output" % (lambdas[l], eta, H))
os.system("grep -v '[a-zA-Z]' output | awk '{if(NF==6 && NR>19)print $0}' | awk '{print $3}' >ent")
enthalpy[l] = os.popen("tail -n 1 ent").read()
ee = loadtxt("ent")
aver_enthalpy[l] = mean(ee[-1])
# os.system("mv dump.dcd dump%d.dcd" % exchange)
os.system("mv log.lammps log%d.lammps" % exchange)
os.system("mv final_restart_file final_restart_file%d" % exchange)
os.system("mv ent ent%d" % exchange)
os.system("bzip2 log%d.lammps ent%d" % (exchange,exchange))
os.system("cp final_restart_file%d restart_file" % exchange)
### replicas will be exchanged based on enthalpy order, not replicas order (termostat order)
#entalpy_sorted_indices = enthalpy.argsort()
aver_entalpy_sorted_indices = aver_enthalpy.argsort()
### choose pair of replicas for exchange attempt based on enthalpy order
pp = random.random_integers(0,ll-2)
first = aver_entalpy_sorted_indices[pp]
second = aver_entalpy_sorted_indices[pp+1]
#if (first>second):
# tmp = first
# first = second
# second = tmp
print "pair1:", first, second
### calculate weights for exchange criterion
w1 = log(lambdas[first]+eta*(enthalpy[first]-1*H))
w2 = log(lambdas[first]+eta*(enthalpy[second]-1*H))
w3 = log(lambdas[second]+eta*(enthalpy[first]-1*H))
w4 = log(lambdas[second]+eta*(enthalpy[second]-1*H))
weight = (w4-w3+w1-w2)/eta/kB
### generate randon number for exchange criterion and calc its log
LOGRANDNUM = log(random.random())
### wyzeruj warunki
compare1 = 0
compare2 = 0
if (weight>0):
compare1 = 1
if (weight>LOGRANDNUM):
compare2 = 1
### exchange restart files if exchange condition is satisfied
if (compare1>0 or compare2>0):
print "exchange1 accepted for pair", first, second, lambdas[first], lambdas[second], "with compares as", compare1, compare2, "weight as", weight, "and lograndnum", LOGRANDNUM
os.system("cp %s/%s/final_restart_file%d %s/%s/restart_file" % (path,lambdas[first],exchange,path,lambdas[second]))
os.system("cp %s/%s/final_restart_file%d %s/%s/restart_file" % (path,lambdas[second],exchange,path,lambdas[first]))
### update walkers
tmp1=walker[first]
tmp2=walker[second]
walker[first]=tmp2
walker[second]=tmp1
else:
print "exchange1 not accepted for pair", first, second, lambdas[first], lambdas[second], "with compares as", compare1, compare2, "weight as", weight, "and lograndnum", LOGRANDNUM
### choose again pair of replicas for exchange attempt based on enthalpy order
### but make sure this pair is different than the first pair
if_different = 0
while if_different<1:
pp2 = random.random_integers(0,ll-2)
third = aver_entalpy_sorted_indices[pp2]
fourth = aver_entalpy_sorted_indices[pp2+1]
if (third!=first and third!=second and third!=aver_entalpy_sorted_indices[pp-1]):
if_different = 1
print "pair2:", third, fourth
### calculate weights for exchange criterion
w1 = log(lambdas[third]+eta*(enthalpy[third]-1*H))
w2 = log(lambdas[third]+eta*(enthalpy[fourth]-1*H))
w3 = log(lambdas[fourth]+eta*(enthalpy[third]-1*H))
w4 = log(lambdas[fourth]+eta*(enthalpy[fourth]-1*H))
weight = (w4-w3+w1-w2)/eta/kB
### generate randon number for exchange criterion and calc its log
LOGRANDNUM = log(random.random())
### wyzeruj warunki
compare1 = 0
compare2 = 0
if (weight>0):
compare1 = 1
if (weight>LOGRANDNUM):
compare2 = 1
### exchange restart files if exchange condition is satisfied
if (compare1>0 or compare2>0):
print "exchange2 accepted for pair", third, fourth, lambdas[third], lambdas[fourth], "with compares as", compare1, compare2, "weight as", weight, "and lograndnum", LOGRANDNUM
os.system("cp %s/%s/final_restart_file%d %s/%s/restart_file" % (path,lambdas[third],exchange,path,lambdas[fourth]))
os.system("cp %s/%s/final_restart_file%d %s/%s/restart_file" % (path,lambdas[fourth],exchange,path,lambdas[third]))
### update walkers
tmp1=walker[third]
tmp2=walker[fourth]
walker[third]=tmp2
walker[fourth]=tmp1
else:
print "exchange2 not accepted for pair", third, fourth, lambdas[third], lambdas[fourth], "with compares as", compare1, compare2, "weight as", weight, "and lograndnum", LOGRANDNUM
#print "walkers:", walker
print "".join(["%d " % x for x in walker])
sys.stdout.flush()
lastwalker = open(path + "/lastwalker", "w")
lastwalker.write("".join(["%d " % w for w in walker]))
lastwalker.close()
lastexchange = open(path + "/lastexchange", "w")
lastexchange.write("%d" % (exchange+1))
lastexchange.close()

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# LJ particles
variable T0 index 300.0
variable press index 0.0
variable lambda index 400.0
variable eta index -0.01
variable enthalpy index -30000.0
units real
atom_style full
pair_style lj/cut 5.0
read_data "restart_file"
thermo 10
thermo_style custom step temp pe etotal press vol
velocity all create ${T0} 12427
timestep 1.0
fix fxnvt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0
fix fxgREM all grem ${lambda} ${eta} ${enthalpy} fxnvt
thermo_modify press fxgREM_press
run 10000
write_data final_restart_file

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#!/bin/sh
NPROCS=1
if [ $# -gt 0 ]; then
NPROCS=$1
fi
bash ./clean.sh
python ./double-re-short.py $NPROCS $HOME/compile/lammps-icms/src/lmp_omp in.gREM > total_output.$NPROCS
exit 0

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0 1 2 3 4 5

21
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# LJ particles
variable T0 equal 300.0
variable press equal 0.0
units real
atom_style full
pair_style lj/cut 5.0
read_data "lj.data"
thermo 10
thermo_style custom step temp pe etotal press vol
timestep 1.0
fix fxnpt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0
fix fxgREM all grem 400 -.01 -30000 fxnpt
thermo_modify press fxgREM_press
run 1000
#write_data lj-out.data

20
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# LJ particles
variable T0 equal 300.0
variable press equal 0.0
units real
atom_style full
pair_style lj/cut 5.0
read_data "lj.data"
thermo 10
thermo_style custom step temp pe etotal press vol
timestep 1.0
fix fxnvt all nvt temp ${T0} ${T0} 1000.0
fix fxgREM all grem 400 -.01 -30000 fxnvt
run 1000
#write_data lj-out.data

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LAMMPS (9 Nov 2016)
using 1 OpenMP thread(s) per MPI task
# LJ particles
variable T0 equal 300.0
variable press equal 0.0
units real
atom_style full
pair_style lj/cut 5.0
read_data "lj.data"
orthogonal box = (1.06874 1.06874 1.06874) to (23.9313 23.9313 23.9313)
1 by 1 by 1 MPI processor grid
reading atoms ...
500 atoms
reading velocities ...
500 velocities
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
thermo 10
thermo_style custom step temp pe etotal press vol
timestep 1.0
fix fxnvt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0
fix fxnvt all npt temp 300 ${T0} 1000.0 iso ${press} ${press} 10000.0
fix fxnvt all npt temp 300 300 1000.0 iso ${press} ${press} 10000.0
fix fxnvt all npt temp 300 300 1000.0 iso 0 ${press} 10000.0
fix fxnvt all npt temp 300 300 1000.0 iso 0 0 10000.0
fix fxgREM all grem 400 -.01 -30000 fxnvt
thermo_modify press fxgREM_press
run 1000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7
ghost atom cutoff = 7
binsize = 3.5 -> bins = 7 7 7
Memory usage per processor = 5.37943 Mbytes
Step Temp PotEng TotEng Press Volume
0 305.69499 -3177.6423 -2722.9442 -91.741776 11950.115
10 312.30124 -3182.2257 -2717.7013 -203.95075 11950.113
20 314.94567 -3186.456 -2717.9982 -265.56737 11950.108
30 312.229 -3183.7641 -2719.3472 -196.90499 11950.097
40 305.94068 -3180.7085 -2725.6449 -92.562221 11950.083
50 300.42281 -3176.5838 -2729.7277 10.896769 11950.066
60 299.16747 -3174.1939 -2729.205 50.094171 11950.05
70 301.65965 -3176.0918 -2727.396 0.096901939 11950.035
80 304.77876 -3178.2699 -2724.9346 -64.001022 11950.019
90 305.60598 -3178.9517 -2724.386 -93.672879 11950.003
100 303.8005 -3177.5156 -2725.6354 -74.516709 11949.985
110 300.86776 -3175.4773 -2727.9593 -34.22655 11949.965
120 298.70177 -3175.6488 -2731.3526 -19.014898 11949.944
130 298.39686 -3176.3792 -2732.5365 -21.293245 11949.923
140 300.00669 -3177.7032 -2731.466 -40.992937 11949.902
150 301.85665 -3178.1312 -2729.1423 -45.715505 11949.88
160 301.20597 -3177.3218 -2729.3007 -10.104082 11949.857
170 297.01134 -3172.7462 -2730.9643 99.298381 11949.833
180 291.279 -3168.3513 -2735.0958 219.47549 11949.812
190 287.13954 -3165.1287 -2738.0304 309.36947 11949.796
200 286.57735 -3165.2951 -2739.033 323.96954 11949.786
210 289.83941 -3167.8245 -2736.7103 271.77305 11949.783
220 296.12858 -3171.8054 -2731.3366 172.4056 11949.785
230 303.82424 -3176.3108 -2724.3952 56.711479 11949.791
240 309.95738 -3180.9789 -2719.9408 -40.992898 11949.798
250 312.0405 -3182.3473 -2718.2107 -57.591676 11949.805
260 309.65444 -3181.0587 -2720.4712 3.3540332 11949.81
270 304.40001 -3176.5798 -2723.8078 130.77028 11949.816
280 298.65985 -3174.1505 -2729.9166 237.63562 11949.825
290 294.78709 -3170.9701 -2732.4966 326.94924 11949.838
300 294.03216 -3169.9567 -2732.6062 349.85486 11949.859
310 296.44397 -3172.8519 -2731.914 284.80897 11949.886
320 301.41027 -3175.9697 -2727.6447 179.4647 11949.92
330 307.88911 -3181.2615 -2723.2998 24.702414 11949.957
340 314.73138 -3186.0047 -2717.8656 -132.6263 11949.995
350 320.55591 -3187.8509 -2711.0483 -245.88468 11950.031
360 323.50274 -3188.9994 -2707.8136 -314.73676 11950.062
370 321.61539 -3187.1233 -2708.7448 -293.17446 11950.086
380 314.37275 -3181.484 -2713.8784 -169.00448 11950.104
390 303.54884 -3174.1675 -2722.6616 12.923999 11950.119
400 293.40432 -3167.0348 -2730.6181 187.6624 11950.135
410 288.46351 -3165.273 -2736.2054 252.20051 11950.154
420 290.31387 -3168.604 -2736.7841 193.73816 11950.178
430 296.35519 -3173.09 -2732.2841 81.521847 11950.207
440 301.92973 -3175.4344 -2726.3368 -1.8329439 11950.237
450 303.76205 -3176.777 -2724.9539 -35.002096 11950.267
460 301.71619 -3174.2731 -2725.4932 14.977875 11950.296
470 298.92404 -3172.9921 -2728.3652 64.224747 11950.326
480 298.80164 -3172.5329 -2728.0881 82.781347 11950.358
490 302.71589 -3175.3703 -2725.1034 27.223049 11950.39
500 309.10665 -3179.3013 -2719.5285 -65.460658 11950.424
510 314.36408 -3183.2854 -2715.6927 -151.19245 11950.456
520 315.71154 -3183.5328 -2713.9358 -163.19151 11950.485
530 313.31886 -3182.2521 -2716.214 -125.5741 11950.511
540 309.81847 -3178.9358 -2718.1043 -55.55841 11950.534
550 308.29687 -3177.837 -2719.2688 -24.39371 11950.556
560 308.75927 -3176.3265 -2717.0705 0.93689833 11950.578
570 307.52811 -3175.8145 -2718.3897 35.502429 11950.6
580 301.75074 -3173.1208 -2724.2894 136.29625 11950.622
590 292.37743 -3165.5806 -2730.6913 319.75957 11950.648
600 283.57627 -3159.8617 -2738.0635 471.28045 11950.68
610 279.85172 -3157.4557 -2741.1975 530.72699 11950.722
620 283.40879 -3160.5911 -2739.042 455.28104 11950.775
630 292.53718 -3166.3125 -2731.1856 296.63465 11950.838
640 302.81112 -3173.3096 -2722.901 113.80844 11950.907
650 309.83321 -3179.3684 -2718.515 -26.499431 11950.978
660 312.1283 -3182.7335 -2718.4663 -89.363745 11951.049
670 311.16363 -3181.867 -2719.0347 -69.370989 11951.118
680 308.51041 -3180.6869 -2721.801 -25.972987 11951.186
690 304.64393 -3176.8751 -2723.7403 56.592367 11951.254
700 300.24456 -3175.4797 -2728.8887 112.34442 11951.323
710 296.35785 -3172.9705 -2732.1607 168.18009 11951.394
720 293.78145 -3172.1065 -2735.1289 182.81082 11951.468
730 293.25707 -3170.8715 -2734.6738 171.04236 11951.547
740 295.33219 -3172.9109 -2733.6266 91.351362 11951.629
750 299.69136 -3175.2574 -2729.4892 -16.266404 11951.713
760 305.2281 -3177.9836 -2723.9799 -137.30615 11951.796
770 310.59309 -3182.7053 -2720.7216 -272.72961 11951.877
780 314.65573 -3183.4212 -2715.3947 -341.231 11951.952
790 316.48606 -3185.44 -2714.691 -388.53602 11952.02
800 315.15897 -3186.846 -2718.0709 -384.28316 11952.08
810 310.43559 -3183.6648 -2721.9154 -282.61999 11952.133
820 303.22265 -3178.464 -2727.4433 -121.47565 11952.179
830 295.36843 -3175.4771 -2736.1389 33.066504 11952.223
840 288.69698 -3169.5813 -2740.1664 216.10697 11952.268
850 283.82649 -3165.7822 -2743.6118 359.56896 11952.317
860 280.04102 -3162.8228 -2746.283 475.61942 11952.374
870 277.10059 -3159.6212 -2747.4551 572.5432 11952.441
880 275.76549 -3158.2545 -2748.0743 616.43304 11952.52
890 276.82327 -3158.9703 -2747.2166 596.08147 11952.612
900 280.72135 -3162.0637 -2744.5119 506.33695 11952.716
910 287.1035 -3167.4388 -2740.3941 356.68688 11952.831
920 294.28041 -3171.6218 -2733.902 206.06394 11952.953
930 300.36009 -3173.9046 -2727.1418 88.047911 11953.08
940 303.86761 -3175.5599 -2723.5798 7.6846808 11953.209
950 304.42957 -3176.0831 -2723.2672 -25.15496 11953.339
960 303.13982 -3176.0534 -2725.1559 -28.715178 11953.467
970 302.30166 -3176.9758 -2727.325 -43.264668 11953.596
980 303.93331 -3178.9891 -2726.9114 -88.434034 11953.723
990 307.36223 -3180.7316 -2723.5535 -145.46208 11953.849
1000 310.09574 -3181.101 -2719.8571 -180.39125 11953.972
Loop time of 0.307225 on 1 procs for 1000 steps with 500 atoms
Performance: 281.227 ns/day, 0.085 hours/ns, 3254.944 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.25351 | 0.25351 | 0.25351 | 0.0 | 82.52
Bond | 7.1526e-05 | 7.1526e-05 | 7.1526e-05 | 0.0 | 0.02
Neigh | 0.0042093 | 0.0042093 | 0.0042093 | 0.0 | 1.37
Comm | 0.010211 | 0.010211 | 0.010211 | 0.0 | 3.32
Output | 0.0013611 | 0.0013611 | 0.0013611 | 0.0 | 0.44
Modify | 0.033891 | 0.033891 | 0.033891 | 0.0 | 11.03
Other | | 0.003969 | | | 1.29
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1610 ave 1610 max 1610 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 14765 ave 14765 max 14765 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 14765
Ave neighs/atom = 29.53
Ave special neighs/atom = 0
Neighbor list builds = 5
Dangerous builds = 0
#write_data lj-out.data
Total wall time: 0:00:00

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LAMMPS (9 Nov 2016)
using 1 OpenMP thread(s) per MPI task
# LJ particles
variable T0 equal 300.0
variable press equal 0.0
units real
atom_style full
pair_style lj/cut 5.0
read_data "lj.data"
orthogonal box = (1.06874 1.06874 1.06874) to (23.9313 23.9313 23.9313)
1 by 2 by 2 MPI processor grid
reading atoms ...
500 atoms
reading velocities ...
500 velocities
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
thermo 10
thermo_style custom step temp pe etotal press vol
timestep 1.0
fix fxnvt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0
fix fxnvt all npt temp 300 ${T0} 1000.0 iso ${press} ${press} 10000.0
fix fxnvt all npt temp 300 300 1000.0 iso ${press} ${press} 10000.0
fix fxnvt all npt temp 300 300 1000.0 iso 0 ${press} 10000.0
fix fxnvt all npt temp 300 300 1000.0 iso 0 0 10000.0
fix fxgREM all grem 400 -.01 -30000 fxnvt
thermo_modify press fxgREM_press
run 1000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7
ghost atom cutoff = 7
binsize = 3.5 -> bins = 7 7 7
Memory usage per processor = 5.34276 Mbytes
Step Temp PotEng TotEng Press Volume
0 305.69499 -3177.6423 -2722.9442 -91.741776 11950.115
10 312.30124 -3182.2257 -2717.7013 -203.95075 11950.113
20 314.94567 -3186.456 -2717.9982 -265.56737 11950.108
30 312.229 -3183.7641 -2719.3472 -196.90499 11950.097
40 305.94068 -3180.7085 -2725.6449 -92.562221 11950.083
50 300.42281 -3176.5838 -2729.7277 10.896769 11950.066
60 299.16747 -3174.1939 -2729.205 50.094171 11950.05
70 301.65965 -3176.0918 -2727.396 0.096901939 11950.035
80 304.77876 -3178.2699 -2724.9346 -64.001022 11950.019
90 305.60598 -3178.9517 -2724.386 -93.672879 11950.003
100 303.8005 -3177.5156 -2725.6354 -74.516709 11949.985
110 300.86776 -3175.4773 -2727.9593 -34.22655 11949.965
120 298.70177 -3175.6488 -2731.3526 -19.014898 11949.944
130 298.39686 -3176.3792 -2732.5365 -21.293245 11949.923
140 300.00669 -3177.7032 -2731.466 -40.992937 11949.902
150 301.85665 -3178.1312 -2729.1423 -45.715505 11949.88
160 301.20597 -3177.3218 -2729.3007 -10.104082 11949.857
170 297.01134 -3172.7462 -2730.9643 99.298381 11949.833
180 291.279 -3168.3513 -2735.0958 219.47549 11949.812
190 287.13954 -3165.1287 -2738.0304 309.36947 11949.796
200 286.57735 -3165.2951 -2739.033 323.96954 11949.786
210 289.83941 -3167.8245 -2736.7103 271.77305 11949.783
220 296.12858 -3171.8054 -2731.3366 172.4056 11949.785
230 303.82424 -3176.3108 -2724.3952 56.711479 11949.791
240 309.95738 -3180.9789 -2719.9408 -40.992898 11949.798
250 312.0405 -3182.3473 -2718.2107 -57.591676 11949.805
260 309.65444 -3181.0587 -2720.4712 3.3540332 11949.81
270 304.40001 -3176.5798 -2723.8078 130.77028 11949.816
280 298.65985 -3174.1505 -2729.9166 237.63562 11949.825
290 294.78709 -3170.9701 -2732.4966 326.94924 11949.838
300 294.03216 -3169.9567 -2732.6062 349.85486 11949.859
310 296.44397 -3172.8519 -2731.914 284.80897 11949.886
320 301.41027 -3175.9697 -2727.6447 179.4647 11949.92
330 307.88911 -3181.2615 -2723.2998 24.702414 11949.957
340 314.73138 -3186.0047 -2717.8656 -132.6263 11949.995
350 320.55591 -3187.8509 -2711.0483 -245.88468 11950.031
360 323.50274 -3188.9994 -2707.8136 -314.73676 11950.062
370 321.61539 -3187.1233 -2708.7448 -293.17446 11950.086
380 314.37275 -3181.484 -2713.8784 -169.00448 11950.104
390 303.54884 -3174.1675 -2722.6616 12.923999 11950.119
400 293.40432 -3167.0348 -2730.6181 187.6624 11950.135
410 288.46351 -3165.273 -2736.2054 252.20051 11950.154
420 290.31387 -3168.604 -2736.7841 193.73816 11950.178
430 296.35519 -3173.09 -2732.2841 81.521847 11950.207
440 301.92973 -3175.4344 -2726.3368 -1.8329439 11950.237
450 303.76205 -3176.777 -2724.9539 -35.002096 11950.267
460 301.71619 -3174.2731 -2725.4932 14.977875 11950.296
470 298.92404 -3172.9921 -2728.3652 64.224747 11950.326
480 298.80164 -3172.5329 -2728.0881 82.781347 11950.358
490 302.71589 -3175.3703 -2725.1034 27.223049 11950.39
500 309.10665 -3179.3013 -2719.5285 -65.460658 11950.424
510 314.36408 -3183.2854 -2715.6927 -151.19245 11950.456
520 315.71154 -3183.5328 -2713.9358 -163.19151 11950.485
530 313.31886 -3182.2521 -2716.214 -125.5741 11950.511
540 309.81847 -3178.9358 -2718.1043 -55.55841 11950.534
550 308.29687 -3177.837 -2719.2688 -24.39371 11950.556
560 308.75927 -3176.3265 -2717.0705 0.93689833 11950.578
570 307.52811 -3175.8145 -2718.3897 35.502429 11950.6
580 301.75074 -3173.1208 -2724.2894 136.29625 11950.622
590 292.37743 -3165.5806 -2730.6913 319.75957 11950.648
600 283.57627 -3159.8617 -2738.0635 471.28045 11950.68
610 279.85172 -3157.4557 -2741.1975 530.72699 11950.722
620 283.40879 -3160.5911 -2739.042 455.28104 11950.775
630 292.53718 -3166.3125 -2731.1856 296.63465 11950.838
640 302.81112 -3173.3096 -2722.901 113.80844 11950.907
650 309.83321 -3179.3684 -2718.515 -26.499431 11950.978
660 312.1283 -3182.7335 -2718.4663 -89.363745 11951.049
670 311.16363 -3181.867 -2719.0347 -69.370989 11951.118
680 308.51041 -3180.6869 -2721.801 -25.972987 11951.186
690 304.64393 -3176.8751 -2723.7403 56.592367 11951.254
700 300.24456 -3175.4797 -2728.8887 112.34442 11951.323
710 296.35785 -3172.9705 -2732.1607 168.18009 11951.394
720 293.78145 -3172.1065 -2735.1289 182.81082 11951.468
730 293.25707 -3170.8715 -2734.6738 171.04236 11951.547
740 295.33219 -3172.9109 -2733.6266 91.351362 11951.629
750 299.69136 -3175.2574 -2729.4892 -16.266404 11951.713
760 305.2281 -3177.9836 -2723.9799 -137.30615 11951.796
770 310.59309 -3182.7053 -2720.7216 -272.72961 11951.877
780 314.65573 -3183.4212 -2715.3947 -341.231 11951.952
790 316.48606 -3185.44 -2714.691 -388.53602 11952.02
800 315.15897 -3186.846 -2718.0709 -384.28316 11952.08
810 310.43559 -3183.6648 -2721.9154 -282.61999 11952.133
820 303.22265 -3178.464 -2727.4433 -121.47565 11952.179
830 295.36843 -3175.4771 -2736.1389 33.066504 11952.223
840 288.69698 -3169.5813 -2740.1664 216.10697 11952.268
850 283.82649 -3165.7822 -2743.6118 359.56896 11952.317
860 280.04102 -3162.8228 -2746.283 475.61942 11952.374
870 277.10059 -3159.6212 -2747.4551 572.5432 11952.441
880 275.76549 -3158.2545 -2748.0743 616.43304 11952.52
890 276.82327 -3158.9703 -2747.2166 596.08147 11952.612
900 280.72135 -3162.0637 -2744.5119 506.33695 11952.716
910 287.1035 -3167.4388 -2740.3941 356.68688 11952.831
920 294.28041 -3171.6218 -2733.902 206.06394 11952.953
930 300.36009 -3173.9046 -2727.1418 88.047911 11953.08
940 303.86761 -3175.5599 -2723.5798 7.6846808 11953.209
950 304.42957 -3176.0831 -2723.2672 -25.15496 11953.339
960 303.13982 -3176.0534 -2725.1559 -28.715178 11953.467
970 302.30166 -3176.9758 -2727.325 -43.264668 11953.596
980 303.93331 -3178.9891 -2726.9114 -88.434034 11953.723
990 307.36223 -3180.7316 -2723.5535 -145.46208 11953.849
1000 310.09574 -3181.101 -2719.8571 -180.39125 11953.972
Loop time of 0.154208 on 4 procs for 1000 steps with 500 atoms
Performance: 560.281 ns/day, 0.043 hours/ns, 6484.730 timesteps/s
98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.072079 | 0.074846 | 0.079666 | 1.1 | 48.54
Bond | 5.7936e-05 | 6.634e-05 | 8.1062e-05 | 0.1 | 0.04
Neigh | 0.0010812 | 0.0012064 | 0.0012748 | 0.2 | 0.78
Comm | 0.032452 | 0.037544 | 0.04076 | 1.6 | 24.35
Output | 0.0018461 | 0.0020589 | 0.0026393 | 0.7 | 1.34
Modify | 0.032085 | 0.032688 | 0.033361 | 0.3 | 21.20
Other | | 0.005799 | | | 3.76
Nlocal: 125 ave 127 max 123 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 870.5 ave 882 max 862 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Neighs: 3691.25 ave 3807 max 3563 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Total # of neighbors = 14765
Ave neighs/atom = 29.53
Ave special neighs/atom = 0
Neighbor list builds = 5
Dangerous builds = 0
#write_data lj-out.data
Total wall time: 0:00:00

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LAMMPS (9 Nov 2016)
using 1 OpenMP thread(s) per MPI task
# LJ particles
variable T0 equal 300.0
variable press equal 0.0
units real
atom_style full
pair_style lj/cut 5.0
read_data "lj.data"
orthogonal box = (1.06874 1.06874 1.06874) to (23.9313 23.9313 23.9313)
1 by 1 by 1 MPI processor grid
reading atoms ...
500 atoms
reading velocities ...
500 velocities
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
thermo 10
thermo_style custom step temp pe etotal press vol
timestep 1.0
fix fxnvt all nvt temp ${T0} ${T0} 1000.0
fix fxnvt all nvt temp 300 ${T0} 1000.0
fix fxnvt all nvt temp 300 300 1000.0
fix fxgREM all grem 400 -.01 -30000 fxnvt
run 1000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7
ghost atom cutoff = 7
binsize = 3.5 -> bins = 7 7 7
Memory usage per processor = 5.37943 Mbytes
Step Temp PotEng TotEng Press Volume
0 305.69499 -3177.6423 -2722.9442 883.58369 11950.115
10 312.30121 -3182.2257 -2717.7013 793.47811 11950.115
20 314.94553 -3186.4559 -2717.9983 738.74091 11950.115
30 312.22861 -3183.7638 -2719.3474 797.47978 11950.115
40 305.93987 -3180.7079 -2725.6455 881.30806 11950.115
50 300.42132 -3176.5828 -2729.7288 967.92042 11950.115
60 299.16487 -3174.1921 -2729.2071 1004.247 11950.115
70 301.65565 -3176.0891 -2727.3992 962.58134 11950.115
80 304.77334 -3178.2663 -2724.939 907.8946 11950.115
90 305.59929 -3178.9472 -2724.3914 879.91629 11950.115
100 303.79263 -3177.5103 -2725.6418 892.67631 11950.115
110 300.85863 -3175.4711 -2727.9667 923.44924 11950.115
120 298.69083 -3175.6415 -2731.3615 931.87518 11950.115
130 298.38415 -3176.3706 -2732.5468 928.88286 11950.115
140 299.99129 -3177.6935 -2731.4792 914.36783 11950.115
150 301.83869 -3178.121 -2729.1588 915.01407 11950.115
160 301.18834 -3177.3117 -2729.3169 947.45228 11950.115
170 296.99406 -3172.7363 -2730.9801 1042.6928 11950.115
180 291.25952 -3168.3407 -2735.1142 1144.5436 11950.115
190 287.1178 -3164.9847 -2737.9187 1223.4003 11950.115
200 286.552 -3165.2799 -2739.0555 1235.6703 11950.115
210 289.81033 -3167.8062 -2736.7353 1194.6672 11950.115
220 296.09616 -3171.7847 -2731.3641 1115.8799 11950.115
230 303.79176 -3176.2893 -2724.4221 1024.6471 11950.115
240 309.9273 -3180.9591 -2719.9657 945.55045 11950.115
250 312.0159 -3182.3307 -2718.2306 934.36956 11950.115
260 309.63264 -3181.0452 -2720.4901 986.77385 11950.115
270 304.38172 -3176.568 -2723.8233 1097.264 11950.115
280 298.64188 -3174.1384 -2729.9313 1186.2239 11950.115
290 294.76686 -3170.9562 -2732.5128 1264.247 11950.115
300 294.00805 -3169.8091 -2732.4944 1287.4001 11950.115
310 296.41801 -3172.834 -2731.9347 1229.5624 11950.115
320 301.38477 -3175.9514 -2727.6644 1140.8664 11950.115
330 307.86584 -3181.2442 -2723.3171 1007.1545 11950.115
340 314.7103 -3185.9891 -2717.8814 871.74528 11950.115
350 320.53954 -3187.8385 -2711.0602 776.85994 11950.115
360 323.49505 -3188.9927 -2707.8184 716.58062 11950.115
370 321.62077 -3187.1246 -2708.7381 731.01909 11950.115
380 314.39049 -3181.4931 -2713.8611 831.21057 11950.115
390 303.57079 -3174.1804 -2722.6419 978.62645 11950.115
400 293.42165 -3167.0452 -2730.6027 1122.3558 11950.115
410 288.46838 -3165.4071 -2736.3322 1171.8087 11950.115
420 290.30766 -3168.5988 -2736.7882 1122.5413 11950.115
430 296.34338 -3173.0824 -2732.2941 1030.2769 11950.115
440 301.92394 -3175.4307 -2726.3417 964.25387 11950.115
450 303.76745 -3176.9122 -2725.0811 934.49176 11950.115
460 301.72985 -3174.2821 -2725.4818 979.07605 11950.115
470 298.93736 -3173.0014 -2728.3548 1020.0482 11950.115
480 298.80912 -3172.803 -2728.3471 1036.6531 11950.115
490 302.72217 -3175.3764 -2725.1001 997.71146 11950.115
500 309.11393 -3179.3088 -2719.5253 925.81108 11950.115
510 314.37612 -3183.2961 -2715.6855 856.23748 11950.115
520 315.72767 -3183.547 -2713.926 847.70543 11950.115
530 313.34173 -3182.2695 -2716.1974 877.30842 11950.115
540 309.84312 -3178.9553 -2718.0871 936.69244 11950.115
550 308.3251 -3177.8582 -2719.248 963.93032 11950.115
560 308.79192 -3176.4834 -2717.1788 989.67643 11950.115
570 307.57194 -3175.8464 -2718.3565 1021.0494 11950.115
580 301.8035 -3173.1582 -2724.2483 1102.4893 11950.115
590 292.43425 -3165.751 -2730.7772 1254.7815 11950.115
600 283.62905 -3159.8987 -2738.022 1381.0608 11950.115
610 279.90122 -3157.49 -2741.1581 1431.0028 11950.115
620 283.4582 -3160.756 -2739.1334 1367.7385 11950.115
630 292.58866 -3166.3469 -2731.1435 1241.1194 11950.115
640 302.86585 -3173.4778 -2722.9878 1089.7342 11950.115
650 309.89252 -3179.4078 -2718.4662 972.6359 11950.115
660 312.19165 -3182.7754 -2718.414 916.62037 11950.115
670 311.2287 -3181.9102 -2718.9811 933.79804 11950.115
680 308.57852 -3180.7312 -2721.7441 969.24936 11950.115
690 304.71609 -3176.9196 -2723.6775 1040.2699 11950.115
700 300.31995 -3175.5245 -2728.8213 1082.845 11950.115
710 296.43537 -3173.0166 -2732.0915 1127.4487 11950.115
720 293.86692 -3172.1582 -2735.0535 1135.0215 11950.115
730 293.35611 -3170.9335 -2734.5885 1122.9143 11950.115
740 295.44861 -3172.9862 -2733.5288 1050.995 11950.115
750 299.82732 -3175.3467 -2729.3763 958.31462 11950.115
760 305.37987 -3178.216 -2723.9866 854.1946 11950.115
770 310.75394 -3182.8127 -2720.5898 737.72668 11950.115
780 314.81395 -3183.7905 -2715.5286 679.74198 11950.115
790 316.63339 -3185.8028 -2714.8346 638.48871 11950.115
800 315.2894 -3186.9345 -2717.9654 641.53256 11950.115
810 310.54289 -3183.7383 -2721.8293 728.51241 11950.115
820 303.31439 -3178.7897 -2727.6326 864.45674 11950.115
830 295.46125 -3175.5387 -2736.0625 997.72969 11950.115
840 288.802 -3169.6502 -2740.0791 1160.6622 11950.115
850 283.94785 -3165.8605 -2743.5096 1289.55 11950.115
860 280.17501 -3163.0381 -2746.299 1392.8854 11950.115
870 277.2456 -3159.8429 -2747.4611 1481.3899 11950.115
880 275.93123 -3158.3584 -2747.9316 1523.5374 11950.115
890 277.0215 -3159.2285 -2747.18 1506.1558 11950.115
900 280.96237 -3162.483 -2744.5728 1428.4183 11950.115
910 287.37962 -3167.6183 -2740.1628 1303.0268 11950.115
920 294.56731 -3171.6765 -2733.5299 1177.748 11950.115
930 300.63273 -3174.0842 -2726.9158 1078.7393 11950.115
940 304.10943 -3175.9847 -2723.645 1007.7154 11950.115
950 304.64845 -3176.6263 -2723.4848 976.37917 11950.115
960 303.36343 -3176.4694 -2725.2393 971.40749 11950.115
970 302.57138 -3177.5541 -2727.5021 954.01115 11950.115
980 304.2593 -3179.2101 -2726.6475 919.74949 11950.115
990 307.69959 -3180.9631 -2723.2833 874.9594 11950.115
1000 310.3971 -3181.9675 -2720.2753 842.81184 11950.115
Loop time of 0.279202 on 1 procs for 1000 steps with 500 atoms
Performance: 309.453 ns/day, 0.078 hours/ns, 3581.633 timesteps/s
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.24196 | 0.24196 | 0.24196 | 0.0 | 86.66
Bond | 6.628e-05 | 6.628e-05 | 6.628e-05 | 0.0 | 0.02
Neigh | 0.0043204 | 0.0043204 | 0.0043204 | 0.0 | 1.55
Comm | 0.010242 | 0.010242 | 0.010242 | 0.0 | 3.67
Output | 0.0012252 | 0.0012252 | 0.0012252 | 0.0 | 0.44
Modify | 0.017572 | 0.017572 | 0.017572 | 0.0 | 6.29
Other | | 0.003811 | | | 1.37
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1610 ave 1610 max 1610 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 14767 ave 14767 max 14767 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 14767
Ave neighs/atom = 29.534
Ave special neighs/atom = 0
Neighbor list builds = 5
Dangerous builds = 0
#write_data lj-out.data
Total wall time: 0:00:00

173
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LAMMPS (9 Nov 2016)
using 1 OpenMP thread(s) per MPI task
# LJ particles
variable T0 equal 300.0
variable press equal 0.0
units real
atom_style full
pair_style lj/cut 5.0
read_data "lj.data"
orthogonal box = (1.06874 1.06874 1.06874) to (23.9313 23.9313 23.9313)
1 by 2 by 2 MPI processor grid
reading atoms ...
500 atoms
reading velocities ...
500 velocities
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
thermo 10
thermo_style custom step temp pe etotal press vol
timestep 1.0
fix fxnvt all nvt temp ${T0} ${T0} 1000.0
fix fxnvt all nvt temp 300 ${T0} 1000.0
fix fxnvt all nvt temp 300 300 1000.0
fix fxgREM all grem 400 -.01 -30000 fxnvt
run 1000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7
ghost atom cutoff = 7
binsize = 3.5 -> bins = 7 7 7
Memory usage per processor = 5.34276 Mbytes
Step Temp PotEng TotEng Press Volume
0 305.69499 -3177.6423 -2722.9442 883.58369 11950.115
10 312.30121 -3182.2257 -2717.7013 793.47811 11950.115
20 314.94553 -3186.4559 -2717.9983 738.74091 11950.115
30 312.22861 -3183.7638 -2719.3474 797.47978 11950.115
40 305.93987 -3180.7079 -2725.6455 881.30806 11950.115
50 300.42132 -3176.5828 -2729.7288 967.92042 11950.115
60 299.16487 -3174.1921 -2729.2071 1004.247 11950.115
70 301.65565 -3176.0891 -2727.3992 962.58134 11950.115
80 304.77334 -3178.2663 -2724.939 907.8946 11950.115
90 305.59929 -3178.9472 -2724.3914 879.91629 11950.115
100 303.79263 -3177.5103 -2725.6418 892.67631 11950.115
110 300.85863 -3175.4711 -2727.9667 923.44924 11950.115
120 298.69083 -3175.6415 -2731.3615 931.87518 11950.115
130 298.38415 -3176.3706 -2732.5468 928.88286 11950.115
140 299.99129 -3177.6935 -2731.4792 914.36783 11950.115
150 301.83869 -3178.121 -2729.1588 915.01407 11950.115
160 301.18834 -3177.3117 -2729.3169 947.45228 11950.115
170 296.99406 -3172.7363 -2730.9801 1042.6928 11950.115
180 291.25952 -3168.3407 -2735.1142 1144.5436 11950.115
190 287.1178 -3164.9847 -2737.9187 1223.4003 11950.115
200 286.552 -3165.2799 -2739.0555 1235.6703 11950.115
210 289.81033 -3167.8062 -2736.7353 1194.6672 11950.115
220 296.09616 -3171.7847 -2731.3641 1115.8799 11950.115
230 303.79176 -3176.2893 -2724.4221 1024.6471 11950.115
240 309.9273 -3180.9591 -2719.9657 945.55045 11950.115
250 312.0159 -3182.3307 -2718.2306 934.36956 11950.115
260 309.63264 -3181.0452 -2720.4901 986.77385 11950.115
270 304.38172 -3176.568 -2723.8233 1097.264 11950.115
280 298.64188 -3174.1384 -2729.9313 1186.2239 11950.115
290 294.76686 -3170.9562 -2732.5128 1264.247 11950.115
300 294.00805 -3169.8091 -2732.4944 1287.4001 11950.115
310 296.41801 -3172.834 -2731.9347 1229.5624 11950.115
320 301.38477 -3175.9514 -2727.6644 1140.8664 11950.115
330 307.86584 -3181.2442 -2723.3171 1007.1545 11950.115
340 314.7103 -3185.9891 -2717.8814 871.74528 11950.115
350 320.53954 -3187.8385 -2711.0602 776.85994 11950.115
360 323.49505 -3188.9927 -2707.8184 716.58062 11950.115
370 321.62077 -3187.1246 -2708.7381 731.01909 11950.115
380 314.39049 -3181.4931 -2713.8611 831.21057 11950.115
390 303.57079 -3174.1804 -2722.6419 978.62645 11950.115
400 293.42165 -3167.0452 -2730.6027 1122.3558 11950.115
410 288.46838 -3165.4071 -2736.3322 1171.8087 11950.115
420 290.30766 -3168.5988 -2736.7882 1122.5413 11950.115
430 296.34338 -3173.0824 -2732.2941 1030.2769 11950.115
440 301.92394 -3175.4307 -2726.3417 964.25387 11950.115
450 303.76745 -3176.9122 -2725.0811 934.49176 11950.115
460 301.72985 -3174.2821 -2725.4818 979.07605 11950.115
470 298.93736 -3173.0014 -2728.3548 1020.0482 11950.115
480 298.80912 -3172.803 -2728.3471 1036.6531 11950.115
490 302.72217 -3175.3764 -2725.1001 997.71146 11950.115
500 309.11393 -3179.3088 -2719.5253 925.81108 11950.115
510 314.37612 -3183.2961 -2715.6855 856.23748 11950.115
520 315.72767 -3183.547 -2713.926 847.70543 11950.115
530 313.34173 -3182.2695 -2716.1974 877.30842 11950.115
540 309.84312 -3178.9553 -2718.0871 936.69244 11950.115
550 308.3251 -3177.8582 -2719.248 963.93032 11950.115
560 308.79192 -3176.4834 -2717.1788 989.67643 11950.115
570 307.57194 -3175.8464 -2718.3565 1021.0494 11950.115
580 301.8035 -3173.1582 -2724.2483 1102.4893 11950.115
590 292.43425 -3165.751 -2730.7772 1254.7815 11950.115
600 283.62905 -3159.8987 -2738.022 1381.0608 11950.115
610 279.90122 -3157.49 -2741.1581 1431.0028 11950.115
620 283.4582 -3160.756 -2739.1334 1367.7385 11950.115
630 292.58866 -3166.3469 -2731.1435 1241.1194 11950.115
640 302.86585 -3173.4778 -2722.9878 1089.7342 11950.115
650 309.89252 -3179.4078 -2718.4662 972.6359 11950.115
660 312.19165 -3182.7754 -2718.414 916.62037 11950.115
670 311.2287 -3181.9102 -2718.9811 933.79804 11950.115
680 308.57852 -3180.7312 -2721.7441 969.24936 11950.115
690 304.71609 -3176.9196 -2723.6775 1040.2699 11950.115
700 300.31995 -3175.5245 -2728.8213 1082.845 11950.115
710 296.43537 -3173.0166 -2732.0915 1127.4487 11950.115
720 293.86692 -3172.1582 -2735.0535 1135.0215 11950.115
730 293.35611 -3170.9335 -2734.5885 1122.9143 11950.115
740 295.44861 -3172.9862 -2733.5288 1050.995 11950.115
750 299.82732 -3175.3467 -2729.3763 958.31462 11950.115
760 305.37987 -3178.216 -2723.9866 854.1946 11950.115
770 310.75394 -3182.8127 -2720.5898 737.72668 11950.115
780 314.81395 -3183.7905 -2715.5286 679.74198 11950.115
790 316.63339 -3185.8028 -2714.8346 638.48871 11950.115
800 315.2894 -3186.9345 -2717.9654 641.53256 11950.115
810 310.54289 -3183.7383 -2721.8293 728.51241 11950.115
820 303.31439 -3178.7897 -2727.6326 864.45674 11950.115
830 295.46125 -3175.5387 -2736.0625 997.72969 11950.115
840 288.802 -3169.6502 -2740.0791 1160.6622 11950.115
850 283.94785 -3165.8605 -2743.5096 1289.55 11950.115
860 280.17501 -3163.0381 -2746.299 1392.8854 11950.115
870 277.2456 -3159.8429 -2747.4611 1481.3899 11950.115
880 275.93123 -3158.3584 -2747.9316 1523.5374 11950.115
890 277.0215 -3159.2285 -2747.18 1506.1558 11950.115
900 280.96237 -3162.483 -2744.5728 1428.4183 11950.115
910 287.37962 -3167.6183 -2740.1628 1303.0268 11950.115
920 294.56731 -3171.6765 -2733.5299 1177.748 11950.115
930 300.63273 -3174.0842 -2726.9158 1078.7393 11950.115
940 304.10943 -3175.9847 -2723.645 1007.7154 11950.115
950 304.64845 -3176.6263 -2723.4848 976.37917 11950.115
960 303.36343 -3176.4694 -2725.2393 971.40749 11950.115
970 302.57138 -3177.5541 -2727.5021 954.01115 11950.115
980 304.2593 -3179.2101 -2726.6475 919.74949 11950.115
990 307.69959 -3180.9631 -2723.2833 874.9594 11950.115
1000 310.3971 -3181.9675 -2720.2753 842.81184 11950.115
Loop time of 0.133894 on 4 procs for 1000 steps with 500 atoms
Performance: 645.285 ns/day, 0.037 hours/ns, 7468.580 timesteps/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.065271 | 0.071043 | 0.07818 | 1.9 | 53.06
Bond | 5.6505e-05 | 6.5565e-05 | 7.7724e-05 | 0.1 | 0.05
Neigh | 0.0011396 | 0.0012607 | 0.0013669 | 0.2 | 0.94
Comm | 0.033866 | 0.040269 | 0.045386 | 2.6 | 30.08
Output | 0.0019252 | 0.0020776 | 0.0023642 | 0.4 | 1.55
Modify | 0.012141 | 0.013629 | 0.01486 | 0.9 | 10.18
Other | | 0.005549 | | | 4.14
Nlocal: 125 ave 127 max 123 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 871.25 ave 882 max 863 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 3691.75 ave 3808 max 3563 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Total # of neighbors = 14767
Ave neighs/atom = 29.534
Ave special neighs/atom = 0
Neighbor list builds = 5
Dangerous builds = 0
#write_data lj-out.data
Total wall time: 0:00:00

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# LJ particles
variable lambda world 900 910 920 930
variable rep world 0 1 2 3
#variable walker world 0 1 3 2
variable T0 equal 300.0
variable press equal 0.0
units real
atom_style full
pair_style lj/cut 5.0
# LJ particles
log ${rep}/log.lammps.${rep}
print "This is replica: ${rep}"
read_data ${rep}/lj.data
#dump dump all xyz 1000 ${rep}/dump.xyz
fix fxnpt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0
fix fxgREM all grem ${lambda} -.03 -30000 fxnpt
thermo 10
thermo_style custom step temp f_fxgREM pe etotal press vol
thermo_modify press fxgREM_press
timestep 1.0
temper/grem 10000 100 ${lambda} fxgREM fxnpt 10294 98392 #${walker}
#write_data ${rep}/lj-out.data

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Interactive MD example files using the fix imd command
To run the demos, first start the LAMMPS simulation, during
initialization it will stop and wait for an IMD client to
connect. Then launch VMD on the same machine with the respective
script to connect and visualize the running simulation. For example:
mpirun -np 4 lmp_linux -log none -in in.melt_imd &
vmd -e melt_imd-demo.vmd
When exiting VMD, the simulation will either continue or wait
for a new connection depending on whether the "nowait" flag was
activated or not. To terminate the LAMMPS simulation,
type "imd kill" into the VMD command line prompt.
To combine interactive MD with force feedback using a
Novint Falcon game controller, have a look at:
http://sites.google.com/site/akohlmey/software/vrpn-icms
Examples:
melt:
an adapted version of the 3d-LJ melt example.
the VMD visualization contains one highlighted
atom to play with force application through a
mouse: Open the Graphical Representations dialog,
Double-click on the first VDW representation
to disable it, click with the mouse on the blue
atom and - while holding the mouse button down -
drag the atom into some direction. A red arrow
should appear indicating direction and magnitude
of the force. Now double-click on the first VDW
representation again to re-enable the rest of
the atoms and watch the blue atom move.
bucky-plus-cnt:
this is "the buckyball challenge". a demo that
is very popular to demonstrate the use of IMD
with force feedback. The system is a SWCNT with
some atoms fixed in space and five C60 fullerenes
in a reflecting wall box. The challenge is to
push all five buckyballs into the nanotube and
have them stay inside.
deca-ala-solv:
a solvated deca alanin helix. The mouse mode is
preset to move residues instead of individual
atoms. Disable the water rep and grab an atom
from the peptide and drag it to apply forces.
deca-ala:
this is the same system as the previous, but
the fix is only applied to the peptide and thus
the corresponding VMD script needs a different
topology file with the matching number of atoms
to visualize it and receive the IMD data.
In case of problems, contact <akohlmey@gmail.com>.

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#!/usr/local/bin/vmd
# Display settings
display projection Perspective
mol new bucky-plus-cnt-mol.psf type psf first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
mol delrep 0 top
mol representation Licorice 0.3 10.0 10.0
mol color ColorID 7
mol selection {index >= 300}
mol addrep top
mol selection {index < 300}
mol color ColorID 23
mol material Glossy
mol representation VDW 0.600000 15.000000
mol addrep top
mol rename top {Put the balls into the tube}
draw delete all
draw material AOChalky
draw color gray
draw triangle {-36.0 -31.0 -7.0} { 46.0 -31.0 -7.0} { 46.0 31.0 -7.0}
draw triangle {-36.0 -31.0 -7.0} {-36.0 31.0 -7.0} { 46.0 31.0 -7.0}
draw color red
draw triangle {-36.0 -31.0 -7.0} {-36.0 -31.0 7.0} {-36.0 31.0 7.0}
draw triangle {-36.0 -31.0 -7.0} {-36.0 31.0 -7.0} {-36.0 31.0 7.0}
draw triangle { 46.0 -31.0 -7.0} { 46.0 -31.0 7.0} { 46.0 31.0 7.0}
draw triangle { 46.0 -31.0 -7.0} { 46.0 31.0 -7.0} { 46.0 31.0 7.0}
draw triangle {-36.0 -31.0 -7.0} {-36.0 -31.0 7.0} { 46.0 -31.0 7.0}
draw triangle {-36.0 -31.0 -7.0} { 46.0 -31.0 -7.0} { 46.0 -31.0 7.0}
draw triangle {-36.0 31.0 -7.0} {-36.0 31.0 7.0} { 46.0 31.0 7.0}
draw triangle {-36.0 31.0 -7.0} { 46.0 31.0 -7.0} { 46.0 31.0 7.0}
imd connect localhost 6789
after idle {
global env
set env(VMDFULLSCREEN) 1
display resize 1200 900
rotate x by -5
rotate y by -5
axes location off
}

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#!/usr/local/bin/vmd
# Display settings
display projection Orthographic
mol new deca-ala-solv.psf type psf first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
mol delrep 0 top
mol representation Licorice
mol color Name
mol selection {protein}
mol material Glossy
mol addrep top
mol selupdate 0 top 1
mol representation HBonds 4.000000 30.000000 3.000000
mol color ColorID 4
mol selection {same residue as within 3.1 of protein}
mol material Opaque
mol addrep top
mol selupdate 1 top 1
mol representation Lines 2.000000
mol color Name
mol selection {(same residue as within 3.1 of protein) and water}
mol addrep top
mol selupdate 2 top 1
imd connect localhost 5678
sleep 1
display resetview
mouse mode forceres

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PSF
6 !NTITLE
REMARKS original generated structure x-plor psf file
REMARKS 2 patches were applied to the molecule.
REMARKS topology top_all22_prot.rtf
REMARKS segment DAL { first NTER; last CTER; auto angles dihedrals }
REMARKS defaultpatch NTER DAL:1
REMARKS defaultpatch CTER DAL:10
103 !NATOM
1 DAL 1 ALA N NH3 -0.300000 14.0070 0
2 DAL 1 ALA HT1 HC 0.330000 1.0080 0
3 DAL 1 ALA HT2 HC 0.330000 1.0080 0
4 DAL 1 ALA HT3 HC 0.330000 1.0080 0
5 DAL 1 ALA CA CT1 0.210000 12.0110 0
6 DAL 1 ALA HA HB 0.100000 1.0080 0
7 DAL 1 ALA CB CT3 -0.270000 12.0110 0
8 DAL 1 ALA HB1 HA 0.090000 1.0080 0
9 DAL 1 ALA HB2 HA 0.090000 1.0080 0
10 DAL 1 ALA HB3 HA 0.090000 1.0080 0
11 DAL 1 ALA C C 0.510000 12.0110 0
12 DAL 1 ALA O O -0.510000 15.9990 0
13 DAL 2 ALA N NH1 -0.470000 14.0070 0
14 DAL 2 ALA HN H 0.310000 1.0080 0
15 DAL 2 ALA CA CT1 0.070000 12.0110 0
16 DAL 2 ALA HA HB 0.090000 1.0080 0
17 DAL 2 ALA CB CT3 -0.270000 12.0110 0
18 DAL 2 ALA HB1 HA 0.090000 1.0080 0
19 DAL 2 ALA HB2 HA 0.090000 1.0080 0
20 DAL 2 ALA HB3 HA 0.090000 1.0080 0
21 DAL 2 ALA C C 0.510000 12.0110 0
22 DAL 2 ALA O O -0.510000 15.9990 0
23 DAL 3 ALA N NH1 -0.470000 14.0070 0
24 DAL 3 ALA HN H 0.310000 1.0080 0
25 DAL 3 ALA CA CT1 0.070000 12.0110 0
26 DAL 3 ALA HA HB 0.090000 1.0080 0
27 DAL 3 ALA CB CT3 -0.270000 12.0110 0
28 DAL 3 ALA HB1 HA 0.090000 1.0080 0
29 DAL 3 ALA HB2 HA 0.090000 1.0080 0
30 DAL 3 ALA HB3 HA 0.090000 1.0080 0
31 DAL 3 ALA C C 0.510000 12.0110 0
32 DAL 3 ALA O O -0.510000 15.9990 0
33 DAL 4 ALA N NH1 -0.470000 14.0070 0
34 DAL 4 ALA HN H 0.310000 1.0080 0
35 DAL 4 ALA CA CT1 0.070000 12.0110 0
36 DAL 4 ALA HA HB 0.090000 1.0080 0
37 DAL 4 ALA CB CT3 -0.270000 12.0110 0
38 DAL 4 ALA HB1 HA 0.090000 1.0080 0
39 DAL 4 ALA HB2 HA 0.090000 1.0080 0
40 DAL 4 ALA HB3 HA 0.090000 1.0080 0
41 DAL 4 ALA C C 0.510000 12.0110 0
42 DAL 4 ALA O O -0.510000 15.9990 0
43 DAL 5 ALA N NH1 -0.470000 14.0070 0
44 DAL 5 ALA HN H 0.310000 1.0080 0
45 DAL 5 ALA CA CT1 0.070000 12.0110 0
46 DAL 5 ALA HA HB 0.090000 1.0080 0
47 DAL 5 ALA CB CT3 -0.270000 12.0110 0
48 DAL 5 ALA HB1 HA 0.090000 1.0080 0
49 DAL 5 ALA HB2 HA 0.090000 1.0080 0
50 DAL 5 ALA HB3 HA 0.090000 1.0080 0
51 DAL 5 ALA C C 0.510000 12.0110 0
52 DAL 5 ALA O O -0.510000 15.9990 0
53 DAL 6 ALA N NH1 -0.470000 14.0070 0
54 DAL 6 ALA HN H 0.310000 1.0080 0
55 DAL 6 ALA CA CT1 0.070000 12.0110 0
56 DAL 6 ALA HA HB 0.090000 1.0080 0
57 DAL 6 ALA CB CT3 -0.270000 12.0110 0
58 DAL 6 ALA HB1 HA 0.090000 1.0080 0
59 DAL 6 ALA HB2 HA 0.090000 1.0080 0
60 DAL 6 ALA HB3 HA 0.090000 1.0080 0
61 DAL 6 ALA C C 0.510000 12.0110 0
62 DAL 6 ALA O O -0.510000 15.9990 0
63 DAL 7 ALA N NH1 -0.470000 14.0070 0
64 DAL 7 ALA HN H 0.310000 1.0080 0
65 DAL 7 ALA CA CT1 0.070000 12.0110 0
66 DAL 7 ALA HA HB 0.090000 1.0080 0
67 DAL 7 ALA CB CT3 -0.270000 12.0110 0
68 DAL 7 ALA HB1 HA 0.090000 1.0080 0
69 DAL 7 ALA HB2 HA 0.090000 1.0080 0
70 DAL 7 ALA HB3 HA 0.090000 1.0080 0
71 DAL 7 ALA C C 0.510000 12.0110 0
72 DAL 7 ALA O O -0.510000 15.9990 0
73 DAL 8 ALA N NH1 -0.470000 14.0070 0
74 DAL 8 ALA HN H 0.310000 1.0080 0
75 DAL 8 ALA CA CT1 0.070000 12.0110 0
76 DAL 8 ALA HA HB 0.090000 1.0080 0
77 DAL 8 ALA CB CT3 -0.270000 12.0110 0
78 DAL 8 ALA HB1 HA 0.090000 1.0080 0
79 DAL 8 ALA HB2 HA 0.090000 1.0080 0
80 DAL 8 ALA HB3 HA 0.090000 1.0080 0
81 DAL 8 ALA C C 0.510000 12.0110 0
82 DAL 8 ALA O O -0.510000 15.9990 0
83 DAL 9 ALA N NH1 -0.470000 14.0070 0
84 DAL 9 ALA HN H 0.310000 1.0080 0
85 DAL 9 ALA CA CT1 0.070000 12.0110 0
86 DAL 9 ALA HA HB 0.090000 1.0080 0
87 DAL 9 ALA CB CT3 -0.270000 12.0110 0
88 DAL 9 ALA HB1 HA 0.090000 1.0080 0
89 DAL 9 ALA HB2 HA 0.090000 1.0080 0
90 DAL 9 ALA HB3 HA 0.090000 1.0080 0
91 DAL 9 ALA C C 0.510000 12.0110 0
92 DAL 9 ALA O O -0.510000 15.9990 0
93 DAL 10 ALA C CC 0.340000 12.0110 0
94 DAL 10 ALA OT1 OC -0.670000 15.9990 0
95 DAL 10 ALA OT2 OC -0.670000 15.9990 0
96 DAL 10 ALA N NH1 -0.470000 14.0070 0
97 DAL 10 ALA HN H 0.310000 1.0080 0
98 DAL 10 ALA CA CT1 0.070000 12.0110 0
99 DAL 10 ALA HA HB 0.090000 1.0080 0
100 DAL 10 ALA CB CT3 -0.270000 12.0110 0
101 DAL 10 ALA HB1 HA 0.090000 1.0080 0
102 DAL 10 ALA HB2 HA 0.090000 1.0080 0
103 DAL 10 ALA HB3 HA 0.090000 1.0080 0
102 !NBOND: bonds
1 5 2 1 3 1 4 1
5 6 7 5 7 8 7 9
7 10 11 5 11 13 12 11
13 14 13 15 15 16 17 15
17 18 17 19 17 20 21 15
21 23 22 21 23 24 23 25
25 26 27 25 27 28 27 29
27 30 31 25 31 33 32 31
33 34 33 35 35 36 37 35
37 38 37 39 37 40 41 35
41 43 42 41 43 44 43 45
45 46 47 45 47 48 47 49
47 50 51 45 51 53 52 51
53 54 53 55 55 56 57 55
57 58 57 59 57 60 61 55
61 63 62 61 63 64 63 65
65 66 67 65 67 68 67 69
67 70 71 65 71 73 72 71
73 74 73 75 75 76 77 75
77 78 77 79 77 80 81 75
81 83 82 81 83 84 83 85
85 86 87 85 87 88 87 89
87 90 91 85 91 96 92 91
93 95 93 94 93 98 96 97
96 98 98 99 100 98 100 101
100 102 100 103
183 !NTHETA: angles
1 5 6 1 5 11 2 1 5
2 1 4 2 1 3 3 1 5
3 1 4 4 1 5 5 11 12
5 11 13 5 7 10 5 7 9
5 7 8 7 5 6 7 5 11
7 5 1 8 7 10 8 7 9
9 7 10 11 5 6 13 15 16
13 15 21 13 11 12 14 13 11
14 13 15 15 21 22 15 21 23
15 17 20 15 17 19 15 17 18
15 13 11 17 15 16 17 15 21
17 15 13 18 17 20 18 17 19
19 17 20 21 15 16 23 25 26
23 25 31 23 21 22 24 23 21
24 23 25 25 31 32 25 31 33
25 27 30 25 27 29 25 27 28
25 23 21 27 25 26 27 25 31
27 25 23 28 27 30 28 27 29
29 27 30 31 25 26 33 35 36
33 35 41 33 31 32 34 33 31
34 33 35 35 41 42 35 41 43
35 37 40 35 37 39 35 37 38
35 33 31 37 35 36 37 35 41
37 35 33 38 37 40 38 37 39
39 37 40 41 35 36 43 45 46
43 45 51 43 41 42 44 43 41
44 43 45 45 51 52 45 51 53
45 47 50 45 47 49 45 47 48
45 43 41 47 45 46 47 45 51
47 45 43 48 47 50 48 47 49
49 47 50 51 45 46 53 55 56
53 55 61 53 51 52 54 53 51
54 53 55 55 61 62 55 61 63
55 57 60 55 57 59 55 57 58
55 53 51 57 55 56 57 55 61
57 55 53 58 57 60 58 57 59
59 57 60 61 55 56 63 65 66
63 65 71 63 61 62 64 63 61
64 63 65 65 71 72 65 71 73
65 67 70 65 67 69 65 67 68
65 63 61 67 65 66 67 65 71
67 65 63 68 67 70 68 67 69
69 67 70 71 65 66 73 75 76
73 75 81 73 71 72 74 73 71
74 73 75 75 81 82 75 81 83
75 77 80 75 77 79 75 77 78
75 73 71 77 75 76 77 75 81
77 75 73 78 77 80 78 77 79
79 77 80 81 75 76 83 85 86
83 85 91 83 81 82 84 83 81
84 83 85 85 91 92 85 91 96
85 87 90 85 87 89 85 87 88
85 83 81 87 85 86 87 85 91
87 85 83 88 87 90 88 87 89
89 87 90 91 85 86 93 98 99
94 93 98 95 93 98 95 93 94
96 98 99 96 98 93 96 91 92
97 96 91 97 96 98 98 100 103
98 100 102 98 100 101 98 96 91
100 98 99 100 98 93 100 98 96
101 100 103 101 100 102 102 100 103
249 !NPHI: dihedrals
1 5 7 8 1 5 7 9
1 5 7 10 1 5 11 13
1 5 11 12 2 1 5 7
2 1 5 11 2 1 5 6
3 1 5 7 3 1 5 11
3 1 5 6 4 1 5 7
4 1 5 11 4 1 5 6
5 11 13 14 5 11 13 15
6 5 7 8 6 5 7 9
6 5 7 10 6 5 11 13
6 5 11 12 7 5 11 13
7 5 11 12 8 7 5 11
9 7 5 11 10 7 5 11
11 13 15 17 11 13 15 21
11 13 15 16 12 11 13 14
12 11 13 15 13 15 17 18
13 15 17 19 13 15 17 20
13 15 21 23 13 15 21 22
14 13 15 17 14 13 15 21
14 13 15 16 15 21 23 24
15 21 23 25 16 15 17 18
16 15 17 19 16 15 17 20
16 15 21 23 16 15 21 22
17 15 21 23 17 15 21 22
18 17 15 21 19 17 15 21
20 17 15 21 21 23 25 27
21 23 25 31 21 23 25 26
22 21 23 24 22 21 23 25
23 25 27 28 23 25 27 29
23 25 27 30 23 25 31 33
23 25 31 32 24 23 25 27
24 23 25 31 24 23 25 26
25 31 33 34 25 31 33 35
26 25 27 28 26 25 27 29
26 25 27 30 26 25 31 33
26 25 31 32 27 25 31 33
27 25 31 32 28 27 25 31
29 27 25 31 30 27 25 31
31 33 35 37 31 33 35 41
31 33 35 36 32 31 33 34
32 31 33 35 33 35 37 38
33 35 37 39 33 35 37 40
33 35 41 43 33 35 41 42
34 33 35 37 34 33 35 41
34 33 35 36 35 41 43 44
35 41 43 45 36 35 37 38
36 35 37 39 36 35 37 40
36 35 41 43 36 35 41 42
37 35 41 43 37 35 41 42
38 37 35 41 39 37 35 41
40 37 35 41 41 43 45 47
41 43 45 51 41 43 45 46
42 41 43 44 42 41 43 45
43 45 47 48 43 45 47 49
43 45 47 50 43 45 51 53
43 45 51 52 44 43 45 47
44 43 45 51 44 43 45 46
45 51 53 54 45 51 53 55
46 45 47 48 46 45 47 49
46 45 47 50 46 45 51 53
46 45 51 52 47 45 51 53
47 45 51 52 48 47 45 51
49 47 45 51 50 47 45 51
51 53 55 57 51 53 55 61
51 53 55 56 52 51 53 54
52 51 53 55 53 55 57 58
53 55 57 59 53 55 57 60
53 55 61 63 53 55 61 62
54 53 55 57 54 53 55 61
54 53 55 56 55 61 63 64
55 61 63 65 56 55 57 58
56 55 57 59 56 55 57 60
56 55 61 63 56 55 61 62
57 55 61 63 57 55 61 62
58 57 55 61 59 57 55 61
60 57 55 61 61 63 65 67
61 63 65 71 61 63 65 66
62 61 63 64 62 61 63 65
63 65 67 68 63 65 67 69
63 65 67 70 63 65 71 73
63 65 71 72 64 63 65 67
64 63 65 71 64 63 65 66
65 71 73 74 65 71 73 75
66 65 67 68 66 65 67 69
66 65 67 70 66 65 71 73
66 65 71 72 67 65 71 73
67 65 71 72 68 67 65 71
69 67 65 71 70 67 65 71
71 73 75 77 71 73 75 81
71 73 75 76 72 71 73 74
72 71 73 75 73 75 77 78
73 75 77 79 73 75 77 80
73 75 81 83 73 75 81 82
74 73 75 77 74 73 75 81
74 73 75 76 75 81 83 84
75 81 83 85 76 75 77 78
76 75 77 79 76 75 77 80
76 75 81 83 76 75 81 82
77 75 81 83 77 75 81 82
78 77 75 81 79 77 75 81
80 77 75 81 81 83 85 87
81 83 85 91 81 83 85 86
82 81 83 84 82 81 83 85
83 85 87 88 83 85 87 89
83 85 87 90 83 85 91 96
83 85 91 92 84 83 85 87
84 83 85 91 84 83 85 86
85 91 96 97 85 91 96 98
86 85 87 88 86 85 87 89
86 85 87 90 86 85 91 96
86 85 91 92 87 85 91 96
87 85 91 92 88 87 85 91
89 87 85 91 90 87 85 91
91 96 98 100 91 96 98 93
91 96 98 99 92 91 96 97
92 91 96 98 93 98 100 101
93 98 100 102 93 98 100 103
93 98 96 97 94 93 98 100
94 93 98 96 94 93 98 99
95 93 98 100 95 93 98 96
95 93 98 99 96 98 100 101
96 98 100 102 96 98 100 103
97 96 98 100 97 96 98 99
99 98 100 101 99 98 100 102
99 98 100 103
19 !NIMPHI: impropers
11 5 13 12 13 11 15 14
21 15 23 22 23 21 25 24
31 25 33 32 33 31 35 34
41 35 43 42 43 41 45 44
51 45 53 52 53 51 55 54
61 55 63 62 63 61 65 64
71 65 73 72 73 71 75 74
81 75 83 82 83 81 85 84
91 85 96 92 93 98 95 94
96 91 98 97
0 !NDON: donors
0 !NACC: acceptors
0 !NNB
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0
1 0 !NGRP
0 0 0

16
examples/PACKAGES/imd/deca-ala_imd-demo.vmd Normal file
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#!/usr/local/bin/vmd
# Display settings
display projection Orthographic
mol new deca-ala.psf type psf first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
mol delrep 0 top
mol representation Licorice
mol color Name
mol selection {all}
mol material Glossy
mol addrep top
imd connect localhost 5678
sleep 1
display resetview
mouse mode forceres

10
examples/PACKAGES/imd/falcon.tcl Normal file
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#!/usr/local/bin/vmd
menu tool on
tool create tug falcon0 fbuttons0 ffeedback0
tool scale 50.0 0
# tool scaleforce 50.0 0
# tool scalespring 35.0
tool scaleforce 15.0 0
tool scalespring 15.0
tool rep 0 -1 -1

59
examples/PACKAGES/imd/in.bucky-plus-cnt Normal file
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# stick a buckyball into a nanotube
units real
dimension 3
boundary f f f
atom_style molecular
newton on off
processors * * 1
# read topology
read_data data.bucky-plus-cnt
pair_style lj/cut 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
special_bonds lj/coul 0.0 0.0 0.0
pair_coeff 1 1 0.07 3.55
pair_coeff 1 2 0.07 3.55
pair_coeff 2 2 0.07 3.55
bond_coeff 1 305.0 1.4
angle_coeff 1 40.000 120.00 35.00 2.41620
dihedral_coeff 1 3.100 2 180 0.0
neighbor 4.0 bin
neigh_modify delay 0 every 1 check yes
timestep 2.0
# we only move some atoms.
group mobile type 1
# have balls bounce off the walls
fix walls mobile wall/reflect xlo EDGE ylo EDGE zlo EDGE xhi EDGE yhi EDGE zhi EDGE
velocity mobile create 303.0 46659 mom yes rot yes dist gaussian
# take some potential energy out of the system
minimize 1.0e-4 1.0e-6 100 1000
reset_timestep 0
fix integrate mobile nve
fix thermostat mobile langevin 300.0 300.0 2000.0 234624
# IMD setup.
fix comm all imd 6789 unwrap on trate 10
#fix comm all imd 6789 unwrap on trate 10 nowait on
# temperature is based on mobile atoms only
compute mobtemp mobile temp
thermo_style custom step pe ke evdwl emol c_mobtemp spcpu
thermo 1000
thermo_modify norm yes
thermo_modify temp mobtemp
run 100000000

62
examples/PACKAGES/imd/in.bucky-plus-cnt-gpu Normal file
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# stick a buckyball into a nanotube
units real
dimension 3
boundary f f f
atom_style molecular
newton off
processors * * 1
# read topology
read_data data.bucky-plus-cnt
pair_style lj/cut/gpu 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
special_bonds lj/coul 0.0 0.0 0.0
pair_coeff 1 1 0.07 3.55
pair_coeff 1 2 0.07 3.55
pair_coeff 2 2 0.07 3.55
bond_coeff 1 305.0 1.4
angle_coeff 1 40.000 120.00 35.00 2.41620
dihedral_coeff 1 3.100 2 180 0.0
neighbor 2.0 bin
neigh_modify delay 0 every 1 check yes
timestep 2.0
# required for GPU acceleration
fix gpu all gpu force 0 0 1.0
# we only move some atoms.
group mobile type 1
# have balls bounce off the walls
fix walls mobile wall/reflect xlo EDGE ylo EDGE zlo EDGE xhi EDGE yhi EDGE zhi EDGE
velocity mobile create 303.0 46659 mom yes rot yes dist gaussian
# take some potential energy out of the system
minimize 1.0e-4 1.0e-6 100 1000
reset_timestep 0
fix integrate mobile nve
fix thermostat mobile langevin 300.0 300.0 2000.0 234624
# IMD setup.
fix comm all imd 6789 unwrap on trate 10
#fix comm all imd 6789 unwrap on trate 10 nowait on
# temperature is based on mobile atoms only
compute mobtemp mobile temp
thermo_style custom step pe ke evdwl emol c_mobtemp spcpu
thermo 1000
thermo_modify norm yes
thermo_modify temp mobtemp
run 100000000

33
examples/PACKAGES/imd/in.deca-ala-solv-filter_imd Normal file
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#
units real
neighbor 2.5 bin
neigh_modify delay 1 every 1
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8 10
pair_modify mix arithmetic
special_bonds charmm
read_data data.deca-ala-solv
group peptide id <= 103
fix rigidh all shake 1e-6 100 1000 t 1 2 3 4 5 a 23
thermo 100
thermo_style multi
timestep 2.0
kspace_style pppm 1e-5
fix ensemble all npt temp 300.0 300.0 100.0 aniso 1.0 1.0 1000.0 drag 0.2
# IMD setup.
fix comm all imd 5678 unwrap on trate 10 filter 20 2
run 5000000

33
examples/PACKAGES/imd/in.deca-ala-solv_imd Normal file
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#
units real
neighbor 2.5 bin
neigh_modify delay 1 every 1
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8 10
pair_modify mix arithmetic
special_bonds charmm
read_data data.deca-ala-solv
group peptide id <= 103
fix rigidh all shake 1e-6 100 1000 t 1 2 3 4 5 a 23
thermo 100
thermo_style multi
timestep 2.0
kspace_style pppm 1e-5
fix ensemble all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 0.2
# IMD setup.
fix comm all imd 5678 unwrap on trate 10
run 5000000

33
examples/PACKAGES/imd/in.deca-ala_imd Normal file
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#
units real
neighbor 2.5 bin
neigh_modify delay 1 every 1
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8 10
pair_modify mix arithmetic
special_bonds charmm
read_data data.deca-ala-solv
group peptide id <= 103
fix rigidh all shake 1e-6 100 1000 t 1 2 3 4 5 a 23
thermo 100
thermo_style multi
timestep 2.0
kspace_style pppm 1e-5
fix ensemble all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 0.2
# IMD setup.
fix comm peptide imd 5678 unwrap on trate 10
run 5000000

35
examples/PACKAGES/imd/in.deca-ala_imd-gpu Normal file
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#
units real
neighbor 2.5 bin
neigh_modify delay 1 every 1
newton off
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long/gpu 8 10
pair_modify mix arithmetic
special_bonds charmm
read_data data.deca-ala-solv
fix 0 all gpu force/neigh 0 0 1.0
group peptide id <= 103
fix rigidh all shake 1e-6 100 1000 t 1 2 3 4 5 a 23
thermo 100
thermo_style multi
timestep 2.0
kspace_style pppm/gpu 1e-5
fix ensemble all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 0.2
# IMD setup.
fix comm peptide imd 5678 unwrap on trate 10
run 5000000

28
examples/PACKAGES/imd/in.melt_imd Normal file
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# 3d Lennard-Jones melt
units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 10 0 10 0 10
create_box 1 box
create_atoms 1 box
mass 1 1.0
velocity all create 3.0 87287
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify every 5 delay 10 check yes
thermo_style custom step pe ke spcpu
fix 1 all nve
# IMD setup.
fix comm all imd 5678 unwrap off fscale 20.0 trate 10 nowait on
thermo 500
run 5000000

30
examples/PACKAGES/imd/in.melt_imd-gpu Normal file
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# 3d Lennard-Jones melt
units lj
atom_style atomic
newton off
lattice fcc 0.8442
region box block 0 10 0 10 0 10
create_box 1 box
create_atoms 1 box
mass 1 1.0
velocity all create 3.0 87287
pair_style lj/cut/gpu 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify every 5 delay 10 check yes
thermo_style custom step pe ke spcpu
fix 0 all gpu force/neigh 0 0 1.0
fix 1 all nve
# IMD setup.
fix comm all imd 5678 unwrap off fscale 20.0 trate 20 nowait on
thermo 500
run 5000000

4532
examples/PACKAGES/imd/melt.psf Normal file
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18
examples/PACKAGES/imd/melt_imd-demo.vmd Normal file
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#!/usr/local/bin/vmd
# Display settings
display projection Orthographic
mol new melt.psf type psf first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
mol delrep 0 top
mol representation VDW 0.400000 8.000000
mol color Name
mol selection {all}
mol material Glossy
mol addrep top
mol selection {index 0}
mol color ColorID 0
mol representation VDW 0.600000 8.000000
mol addrep top
imd connect localhost 5678
mouse mode forceatom

8724
examples/PACKAGES/srp/data.chain Normal file
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42
examples/PACKAGES/srp/in.srp Normal file
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units lj
atom_style full
boundary p p p
special_bonds lj/coul 1 1 1
newton on on
# save an extra atom type for bond particles
read_data data.chain
neighbor 2.0 bin
neigh_modify every 10 check yes
bond_style harmonic
bond_coeff * 225.0 0.85
comm_modify vel yes
comm_modify cutoff 3.6
# must use pair hybrid, since srp bond particles
# do not interact with other atoms types
pair_style hybrid dpd 1.0 1.0 373692 srp 0.8 1 mid
pair_coeff 1 1 dpd 60.0 4.5 1.0
pair_coeff 1 2 none
pair_coeff 2 2 srp 100.0
# auto normalization of thermo quantities is turned off by pair srp
# just divide by natoms
variable natoms equal count(all)
variable nPotEng equal c_thermo_pe/v_natoms
thermo 50
thermo_style custom step temp pe v_nPotEng press atoms v_natoms lx ly lz
fix 1 all nve
timestep 0.01
restart 500 mid-run-*.restart
run 1000
write_restart end-run.restart