From 8a055fdcfa3121b4fbba915b4563e66811997ea9 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 1 Jun 2022 15:04:07 -0400 Subject: [PATCH] merge with third manybody table example and provide updated log files --- examples/PACKAGES/manybody_table/README | 101 +- examples/PACKAGES/manybody_table/in.spce_sw | 20 + .../manybody_table/log.1Jun22.spce.g++.1 | 16 +- .../manybody_table/log.1Jun22.spce.g++.4 | 18 +- .../manybody_table/log.1Jun22.spce2.g++.1 | 18 +- .../manybody_table/log.1Jun22.spce2.g++.4 | 20 +- .../manybody_table/log.1Jun22.spce_sw.g++.1 | 87 ++ .../manybody_table/log.1Jun22.spce_sw.g++.4 | 87 ++ .../spce.sw | 0 .../table_CG_CG_CG.txt | 0 examples/PACKAGES/pair_sw_angle_table/README | 40 - examples/PACKAGES/pair_sw_angle_table/run.sh | 5 - .../PACKAGES/pair_sw_angle_table/spce.data | 1015 -------------- examples/PACKAGES/pair_sw_angle_table/spce.in | 45 - .../pair_sw_angle_table/table_CG_CG.txt | 1203 ----------------- 15 files changed, 276 insertions(+), 2399 deletions(-) create mode 100644 examples/PACKAGES/manybody_table/in.spce_sw create mode 100644 examples/PACKAGES/manybody_table/log.1Jun22.spce_sw.g++.1 create mode 100644 examples/PACKAGES/manybody_table/log.1Jun22.spce_sw.g++.4 rename examples/PACKAGES/{pair_sw_angle_table => manybody_table}/spce.sw (100%) rename examples/PACKAGES/{pair_sw_angle_table => manybody_table}/table_CG_CG_CG.txt (100%) delete mode 100644 examples/PACKAGES/pair_sw_angle_table/README delete mode 100755 examples/PACKAGES/pair_sw_angle_table/run.sh delete mode 100644 examples/PACKAGES/pair_sw_angle_table/spce.data delete mode 100644 examples/PACKAGES/pair_sw_angle_table/spce.in delete mode 100644 examples/PACKAGES/pair_sw_angle_table/table_CG_CG.txt diff --git a/examples/PACKAGES/manybody_table/README b/examples/PACKAGES/manybody_table/README index 3897f80a81..385695e0e0 100644 --- a/examples/PACKAGES/manybody_table/README +++ b/examples/PACKAGES/manybody_table/README @@ -1,65 +1,56 @@ -Example for pair style threebody/table +Three examples inputs for pair styles threebody/table (in.spce and +in.spce2) and sw/angle/table (in.spce_sw). All inputs are for the +simulation of coarse-grained SPC/E water. +A water molecule is represented by one coarse-grained (CG) bead. -This example contains all required input files for the simulation of CG SPC/E water with -the user pair style threebody/table, as well as a run.sh script. - -To run the example, you have to compile LAMMPS with the MANYBODY package, including pair_threebody_table.h and pair_threebody_table.cpp. - -Running the simulations, you will reproduce results of the following publication: - -C. Scherer, R. Scheid, D. Andrienko, and T. Bereau, Kernel-Based Machine Learning for Efficient Simulations of Molecular Liquids, J. Chem. Theor. Comp., 16(5):3194–3204, 2020, https://doi.org/10.1021/acs.jctc.9b01256 - -Here, a water molecule is represented by one coarse-grained (CG) bead. The example contains -two parts. -The three-body (force) tables for both parts (1-1-1.table and 1-1-2.table) have been parametrized with the kernel-based machine learning (ML) with the VOTCA package (https://gitlab.mpcdf.mpg.de/votca/votca). -For a general description of the table format have a look at the documentation of this pair style. -For a example on the parametrization, have a look at https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-examples/guide and +For the two threebody/table examples the three-body (force) tables are +in the files 1-1-1.table and 1-1-2.table. These have been parametrized +with the kernel-based machine learning (ML) with the VOTCA package +(https://gitlab.mpcdf.mpg.de/votca/votca). For a example on the +parametrization, have a look at +https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-examples/guide +and https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-examples/ml. -In both cases, the parametrization is done according to a sample system, using the three-body forces of a Stillinger-Weber potential with tabulated angular forces (sw/angle/table). These then are learned with the covariant meshing technique with the settings files used in https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-examples/ml/3body/with_binning. -For the first part of example, the folder contains the contains the LAMMPS data file (spce.data) with the starting configuration of 1000 CG water molecules, an input file (spce.in) and a threebody file (spce.3b). +In both cases, the parametrization is done according to a sample system, +using the three-body forces of a Stillinger-Weber potential with +tabulated angular forces (sw/angle/table) (see in.spce_sw). These then +are learned with the covariant meshing technique with the settings files +used in +https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-examples/ml/3body/with_binning. -The lammps input file contains the lines specifying the pair style and coefficients: +The first example, in.spce uses the LAMMPS data file (data.spce) with +the starting configuration of 1000 CG water molecules, and a threebody +file (spce.3b) which loads the 1-1-1.table file. -- pair_style hybrid/overlay table linear 1200 threebody/table - use a combination of pair style table with 1200 linear table entries and the pair style threebody/table -- pair_coeff 1 1 table table_CG_CG.txt VOTCA - set the table name and keyword for the pair style table -- pair_coeff * * threebody/table spce.3b type - set the name of threebody file and bead type for the pair style threebody/table +A hybrid/overlay pair style is used to sum a tabulated pairwise +interaction (table_CG_CG.txt) with the tabulated threebody interactions. +The tabulated pair interaction is the effectively the same as in the +what is used by the in.spce_sw input using sw/angle/table pair style. -A hybrid pair style is used, where pair forces are calculated as a tabulated interaction (table_CG_CG.txt) and the pair style threebody/table is only used to calculate the three-body forces. -The tabulated pair interaction is the same as in the example of the sw/angle/table pair style: examples/PACKAGES/pair_sw_angle_table +IMPORTANT NOTE: The threebody tables are parameterized without storing +energies (the last column of the threebody table files is zero). This +is due to a current limitation of the paramerization procedure. -To run the simulation, one needs an additional threebody file (spce.3b). -It has the following structure: +This in.spce2 example uses the data.spce2 file and the threebody input +spce2.3b. This is essentially the same simulation as in in.spce only +the atom type of the first 100 CG water molecules has been changed from +1 to 2. This is done to demonstrate how to run a simulation with +different atom types. -- type - relates to keyword type in LAMMPS input file -- type - relates to keyword type in LAMMPS input file -- type - relates to keyword type in LAMMPS input file -- 3.7 - cutoff in Ang -- 1-1-1.table - name of 3-body force table -- ENTRY1 - keyword in 3-body force table for this interaction -- linear - interpolation is linear -- 12 - number of grid points in radial direction (automatically sets grid size, in this case to 1872) +For this (artificial) two-element simulation, the threebody file now +contain 8 entries for: type1 type1 type1, type1 type1 type2, type1 type2 +type1, type1 type2 type2, type2 type1 type1, type2 type1 type2, type2 +type2 type1, type2 type2 type2. Each entry has the same structure as +above. However, entries where the second and the third element are +different require a different force table (1-1-2.table) instead of +(1-1-1.table). 1-1-2.table contains exactly the force constants as +1-1-1.table. However it has to have the asymmetric structure where both +interparticle distances (r_ij and r_ik) are varied from rmin to rmax and +therefore contains "M = 2 * N * N * N" (2 * 12 * 12 * 12 = 3456) +entries. -As there is only one atom type (1), the force table is symmetric and contains "M = N * N * (N+1)" (12 * 12 * 13 = 1872) entries. - -The LAMMPS simulation is a standard nvt simulation. A dump file is output with the positions and forces every 10 time steps. -You can calculate the pair distribution and compare it to the ones in the publication. - -For the second part of the example, have a look at the LAMMPS data file (spce_2.data), the input file (spce_2.in) and the threebody file (spce_2.3b). -Running the second part, you will in fact perform the same MD simulation as in the first part of the example. However, the atom type of the first 100 CG water molecules has been changed from 1 to 2. -This is done to demonstrate how to run a simulation with different atom types. - -Again, lammps input file (spce_2.in) contains the lines specifying the pair style and coefficients: - -- pair_style hybrid/overlay table linear 1200 threebody/table - use a combination of pair style table with 1200 linear table entries and the pair style threebody/table -- pair_coeff 1 1 table table_CG_CG.txt VOTCA - set the table name and keyword for the pair style table -- pair_coeff * * threebody/table spce_2.3b type1 type2 - set the name of threebody file and bead type for the pair style threebody/table - -Now, the atom type 1 is mapped to the element type1 and the atom type 2 is mapped to the element type2 in the threebody file (spce_2.3b). -For this (artificial) two-element simulation, the threebody file now contain 8 entries for: type1 type1 type1, type1 type1 type2, type1 type2 type1, type1 type2 type2, type2 type1 type1, type2 type1 type2, type2 type2 type1, type2 type2 type2. -Each entry has the same structure as above. However, entries where the second and the third element are different require a different force table (1-1-2.table) instead of (1-1-1.table). -1-1-2.table contains exactly the force constants as 1-1-1.table. -However it has to have the asymmetric structure where both interparticle distances (r_ij and r_ik) are varied from rmin to rmax and therefore contains "M = 2 * N * N * N" (2 * 12 * 12 * 12 = 3456) entries. - -Now run the simulation. The theromodynamic output, as well as, the pair correlation function should be exactly the same as for the first part of the example. +The third example, in.spce_sw, contains the analytical twobody interactions +and replaces the threebody term of the Stillinger-Weber potential with an +angle/table style potential which is stored in the table_CG_CG_CG.txt file. diff --git a/examples/PACKAGES/manybody_table/in.spce_sw b/examples/PACKAGES/manybody_table/in.spce_sw new file mode 100644 index 0000000000..bb0a097743 --- /dev/null +++ b/examples/PACKAGES/manybody_table/in.spce_sw @@ -0,0 +1,20 @@ +units real +atom_style atomic + +read_data data.spce + +pair_style hybrid/overlay table linear 1200 sw/angle/table + +pair_coeff 1 1 table table_CG_CG.txt VOTCA +pair_coeff * * sw/angle/table spce.sw type + +fix 1 all nvt temp 300.0 300.0 200.0 + +velocity all create 300 432567 dist uniform mom yes + +timestep 2.0 + +thermo 100 +#dump 2 all custom 10 spce_sw.dump id type x y z fx fy fz + +run 1000 diff --git a/examples/PACKAGES/manybody_table/log.1Jun22.spce.g++.1 b/examples/PACKAGES/manybody_table/log.1Jun22.spce.g++.1 index 3489ad5d7a..ec20bd3ced 100644 --- a/examples/PACKAGES/manybody_table/log.1Jun22.spce.g++.1 +++ b/examples/PACKAGES/manybody_table/log.1Jun22.spce.g++.1 @@ -57,20 +57,20 @@ Per MPI rank memory allocation (min/avg/max) = 5.487 | 5.487 | 5.487 Mbytes 800 313.16537 -5466.4124 0 -4533.8594 489.99301 900 303.42954 -5506.3208 0 -4602.7595 360.05608 1000 299.50926 -5446.8981 0 -4555.0107 993.95615 -Loop time of 5.12079 on 1 procs for 1000 steps with 1000 atoms +Loop time of 5.15787 on 1 procs for 1000 steps with 1000 atoms -Performance: 33.745 ns/day, 0.711 hours/ns, 195.282 timesteps/s +Performance: 33.502 ns/day, 0.716 hours/ns, 193.879 timesteps/s 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 4.8109 | 4.8109 | 4.8109 | 0.0 | 93.95 -Neigh | 0.27061 | 0.27061 | 0.27061 | 0.0 | 5.28 -Comm | 0.020092 | 0.020092 | 0.020092 | 0.0 | 0.39 -Output | 0.00020325 | 0.00020325 | 0.00020325 | 0.0 | 0.00 -Modify | 0.011643 | 0.011643 | 0.011643 | 0.0 | 0.23 -Other | | 0.007324 | | | 0.14 +Pair | 4.8428 | 4.8428 | 4.8428 | 0.0 | 93.89 +Neigh | 0.27527 | 0.27527 | 0.27527 | 0.0 | 5.34 +Comm | 0.020461 | 0.020461 | 0.020461 | 0.0 | 0.40 +Output | 0.00020949 | 0.00020949 | 0.00020949 | 0.0 | 0.00 +Modify | 0.01198 | 0.01198 | 0.01198 | 0.0 | 0.23 +Other | | 0.007163 | | | 0.14 Nlocal: 1000 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/PACKAGES/manybody_table/log.1Jun22.spce.g++.4 b/examples/PACKAGES/manybody_table/log.1Jun22.spce.g++.4 index e5985ae51e..48b37d55fe 100644 --- a/examples/PACKAGES/manybody_table/log.1Jun22.spce.g++.4 +++ b/examples/PACKAGES/manybody_table/log.1Jun22.spce.g++.4 @@ -57,20 +57,20 @@ Per MPI rank memory allocation (min/avg/max) = 3.87 | 3.87 | 3.87 Mbytes 800 314.09436 -5467.6073 0 -4532.2879 522.73489 900 300.85843 -5503.7551 0 -4607.85 491.78041 1000 302.84638 -5468.3331 0 -4566.5083 338.05123 -Loop time of 1.45119 on 4 procs for 1000 steps with 1000 atoms +Loop time of 1.60997 on 4 procs for 1000 steps with 1000 atoms -Performance: 119.075 ns/day, 0.202 hours/ns, 689.091 timesteps/s -98.3% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 107.331 ns/day, 0.224 hours/ns, 621.131 timesteps/s +94.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.2376 | 1.256 | 1.2833 | 1.5 | 86.55 -Neigh | 0.06865 | 0.06984 | 0.071283 | 0.4 | 4.81 -Comm | 0.084664 | 0.1133 | 0.13329 | 5.4 | 7.81 -Output | 0.0001668 | 0.00034177 | 0.00086454 | 0.0 | 0.02 -Modify | 0.0069024 | 0.0071705 | 0.0074503 | 0.3 | 0.49 -Other | | 0.004489 | | | 0.31 +Pair | 1.28 | 1.2942 | 1.3018 | 0.8 | 80.38 +Neigh | 0.069763 | 0.070222 | 0.070788 | 0.2 | 4.36 +Comm | 0.19379 | 0.20979 | 0.23226 | 3.6 | 13.03 +Output | 0.0001711 | 0.00046947 | 0.0013621 | 0.0 | 0.03 +Modify | 0.021613 | 0.030016 | 0.038718 | 4.8 | 1.86 +Other | | 0.005309 | | | 0.33 Nlocal: 250 ave 257 max 240 min Histogram: 1 0 0 0 0 1 0 0 1 1 diff --git a/examples/PACKAGES/manybody_table/log.1Jun22.spce2.g++.1 b/examples/PACKAGES/manybody_table/log.1Jun22.spce2.g++.1 index 12503118e0..d6432a1c07 100644 --- a/examples/PACKAGES/manybody_table/log.1Jun22.spce2.g++.1 +++ b/examples/PACKAGES/manybody_table/log.1Jun22.spce2.g++.1 @@ -57,20 +57,20 @@ Per MPI rank memory allocation (min/avg/max) = 5.487 | 5.487 | 5.487 Mbytes 800 313.16537 -5466.4124 0 -4533.8594 489.99301 900 303.42954 -5506.3208 0 -4602.7595 360.05608 1000 299.50926 -5446.8981 0 -4555.0107 993.95615 -Loop time of 5.16704 on 1 procs for 1000 steps with 1000 atoms +Loop time of 5.16365 on 1 procs for 1000 steps with 1000 atoms -Performance: 33.443 ns/day, 0.718 hours/ns, 193.534 timesteps/s -99.7% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 33.465 ns/day, 0.717 hours/ns, 193.661 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 4.8574 | 4.8574 | 4.8574 | 0.0 | 94.01 -Neigh | 0.27015 | 0.27015 | 0.27015 | 0.0 | 5.23 -Comm | 0.020112 | 0.020112 | 0.020112 | 0.0 | 0.39 -Output | 0.0002118 | 0.0002118 | 0.0002118 | 0.0 | 0.00 -Modify | 0.011792 | 0.011792 | 0.011792 | 0.0 | 0.23 -Other | | 0.007409 | | | 0.14 +Pair | 4.8443 | 4.8443 | 4.8443 | 0.0 | 93.81 +Neigh | 0.27931 | 0.27931 | 0.27931 | 0.0 | 5.41 +Comm | 0.020302 | 0.020302 | 0.020302 | 0.0 | 0.39 +Output | 0.00022712 | 0.00022712 | 0.00022712 | 0.0 | 0.00 +Modify | 0.011944 | 0.011944 | 0.011944 | 0.0 | 0.23 +Other | | 0.007616 | | | 0.15 Nlocal: 1000 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/PACKAGES/manybody_table/log.1Jun22.spce2.g++.4 b/examples/PACKAGES/manybody_table/log.1Jun22.spce2.g++.4 index 23f3348c34..70fb163b67 100644 --- a/examples/PACKAGES/manybody_table/log.1Jun22.spce2.g++.4 +++ b/examples/PACKAGES/manybody_table/log.1Jun22.spce2.g++.4 @@ -10,7 +10,7 @@ Reading data file ... 1 by 2 by 2 MPI processor grid reading atoms ... 1000 atoms - read_data CPU = 0.002 seconds + read_data CPU = 0.004 seconds pair_style hybrid/overlay table linear 1200 threebody/table @@ -57,20 +57,20 @@ Per MPI rank memory allocation (min/avg/max) = 3.87 | 3.87 | 3.87 Mbytes 800 314.09436 -5467.6073 0 -4532.2879 522.73489 900 300.85843 -5503.7551 0 -4607.85 491.78041 1000 302.84638 -5468.3331 0 -4566.5083 338.05123 -Loop time of 1.4686 on 4 procs for 1000 steps with 1000 atoms +Loop time of 1.54853 on 4 procs for 1000 steps with 1000 atoms -Performance: 117.663 ns/day, 0.204 hours/ns, 680.919 timesteps/s -98.1% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 111.590 ns/day, 0.215 hours/ns, 645.773 timesteps/s +96.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.2491 | 1.2757 | 1.3162 | 2.3 | 86.87 -Neigh | 0.06817 | 0.069468 | 0.071025 | 0.5 | 4.73 -Comm | 0.069929 | 0.11236 | 0.14069 | 8.1 | 7.65 -Output | 0.00016417 | 0.00050711 | 0.0015318 | 0.0 | 0.03 -Modify | 0.0057514 | 0.0061681 | 0.0066503 | 0.5 | 0.42 -Other | | 0.004366 | | | 0.30 +Pair | 1.2599 | 1.2908 | 1.3259 | 2.1 | 83.36 +Neigh | 0.069097 | 0.071294 | 0.075502 | 0.9 | 4.60 +Comm | 0.12731 | 0.15884 | 0.19196 | 5.7 | 10.26 +Output | 0.00017674 | 0.0026016 | 0.0098653 | 8.2 | 0.17 +Modify | 0.0093453 | 0.011999 | 0.014575 | 2.3 | 0.77 +Other | | 0.01295 | | | 0.84 Nlocal: 250 ave 257 max 240 min Histogram: 1 0 0 0 0 1 0 0 1 1 diff --git a/examples/PACKAGES/manybody_table/log.1Jun22.spce_sw.g++.1 b/examples/PACKAGES/manybody_table/log.1Jun22.spce_sw.g++.1 new file mode 100644 index 0000000000..e64d577fae --- /dev/null +++ b/examples/PACKAGES/manybody_table/log.1Jun22.spce_sw.g++.1 @@ -0,0 +1,87 @@ +LAMMPS (4 May 2022) + using 1 OpenMP thread(s) per MPI task +units real +atom_style atomic + +read_data data.spce +Reading data file ... + orthogonal box = (0 0 0) to (31.0648 31.0648 31.0648) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1000 atoms + read_data CPU = 0.001 seconds + +pair_style hybrid/overlay table linear 1200 sw/angle/table + +pair_coeff 1 1 table table_CG_CG.txt VOTCA +pair_coeff * * sw/angle/table spce.sw type + +fix 1 all nvt temp 300.0 300.0 200.0 + +velocity all create 300 432567 dist uniform mom yes + +timestep 2.0 + +thermo 100 +#dump 2 all custom 10 spce_sw.dump id type x y z fx fy fz + +run 1000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair table, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair sw/angle/table, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.487 | 5.487 | 5.487 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 300 -4572.9581 0 -3679.6093 -402.23914 + 100 286.5642 -4508.6912 0 -3655.352 -610.63256 + 200 291.59063 -4465.6368 0 -3597.3297 -218.54913 + 300 298.40301 -4460.64 0 -3572.0468 302.96636 + 400 305.99618 -4460.1128 0 -3548.9084 -68.022415 + 500 301.94233 -4440.337 0 -3541.2043 179.36975 + 600 308.95709 -4485.8412 0 -3565.8197 -95.917517 + 700 291.69015 -4489.4465 0 -3620.843 -56.044939 + 800 294.95653 -4496.904 0 -3618.5738 563.3456 + 900 295.50533 -4478.1134 0 -3598.149 89.234288 + 1000 308.63559 -4471.1612 0 -3552.0971 906.33706 +Loop time of 5.39753 on 1 procs for 1000 steps with 1000 atoms + +Performance: 32.015 ns/day, 0.750 hours/ns, 185.270 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.0954 | 5.0954 | 5.0954 | 0.0 | 94.40 +Neigh | 0.26201 | 0.26201 | 0.26201 | 0.0 | 4.85 +Comm | 0.020497 | 0.020497 | 0.020497 | 0.0 | 0.38 +Output | 0.00021869 | 0.00021869 | 0.00021869 | 0.0 | 0.00 +Modify | 0.011849 | 0.011849 | 0.011849 | 0.0 | 0.22 +Other | | 0.007577 | | | 0.14 + +Nlocal: 1000 ave 1000 max 1000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 5862 ave 5862 max 5862 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 191262 ave 191262 max 191262 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 382524 ave 382524 max 382524 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 382524 +Ave neighs/atom = 382.524 +Neighbor list builds = 26 +Dangerous builds = 0 +Total wall time: 0:00:05 diff --git a/examples/PACKAGES/manybody_table/log.1Jun22.spce_sw.g++.4 b/examples/PACKAGES/manybody_table/log.1Jun22.spce_sw.g++.4 new file mode 100644 index 0000000000..b439b82286 --- /dev/null +++ b/examples/PACKAGES/manybody_table/log.1Jun22.spce_sw.g++.4 @@ -0,0 +1,87 @@ +LAMMPS (4 May 2022) + using 1 OpenMP thread(s) per MPI task +units real +atom_style atomic + +read_data data.spce +Reading data file ... + orthogonal box = (0 0 0) to (31.0648 31.0648 31.0648) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 1000 atoms + read_data CPU = 0.001 seconds + +pair_style hybrid/overlay table linear 1200 sw/angle/table + +pair_coeff 1 1 table table_CG_CG.txt VOTCA +pair_coeff * * sw/angle/table spce.sw type + +fix 1 all nvt temp 300.0 300.0 200.0 + +velocity all create 300 432567 dist uniform mom yes + +timestep 2.0 + +thermo 100 +#dump 2 all custom 10 spce_sw.dump id type x y z fx fy fz + +run 1000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair table, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair sw/angle/table, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.87 | 3.87 | 3.87 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 300 -4572.9581 0 -3679.6093 -402.23914 + 100 286.5642 -4508.6912 0 -3655.352 -610.63256 + 200 291.59063 -4465.6368 0 -3597.3297 -218.54913 + 300 298.40301 -4460.64 0 -3572.0468 302.96636 + 400 305.99618 -4460.1128 0 -3548.9084 -68.022415 + 500 301.94233 -4440.337 0 -3541.2043 179.36975 + 600 308.95709 -4485.8412 0 -3565.8197 -95.917517 + 700 291.69015 -4489.4465 0 -3620.843 -56.044939 + 800 294.95653 -4496.904 0 -3618.5738 563.3456 + 900 295.50533 -4478.1134 0 -3598.149 89.234292 + 1000 308.63559 -4471.1612 0 -3552.0971 906.33708 +Loop time of 1.57073 on 4 procs for 1000 steps with 1000 atoms + +Performance: 110.012 ns/day, 0.218 hours/ns, 636.646 timesteps/s +97.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.3064 | 1.3347 | 1.3706 | 2.0 | 84.97 +Neigh | 0.065344 | 0.070299 | 0.07737 | 1.7 | 4.48 +Comm | 0.117 | 0.15297 | 0.18685 | 6.5 | 9.74 +Output | 0.00016937 | 0.00055648 | 0.0017097 | 0.0 | 0.04 +Modify | 0.0073414 | 0.0079027 | 0.0085343 | 0.6 | 0.50 +Other | | 0.0043 | | | 0.27 + +Nlocal: 250 ave 254 max 247 min +Histogram: 1 1 0 0 0 1 0 0 0 1 +Nghost: 3473.25 ave 3490 max 3450 min +Histogram: 1 0 0 0 0 1 0 1 0 1 +Neighs: 47815.5 ave 48520 max 47134 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +FullNghs: 95631 ave 97203 max 94083 min +Histogram: 1 0 1 0 0 0 1 0 0 1 + +Total # of neighbors = 382524 +Ave neighs/atom = 382.524 +Neighbor list builds = 26 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/PACKAGES/pair_sw_angle_table/spce.sw b/examples/PACKAGES/manybody_table/spce.sw similarity index 100% rename from examples/PACKAGES/pair_sw_angle_table/spce.sw rename to examples/PACKAGES/manybody_table/spce.sw diff --git a/examples/PACKAGES/pair_sw_angle_table/table_CG_CG_CG.txt b/examples/PACKAGES/manybody_table/table_CG_CG_CG.txt similarity index 100% rename from examples/PACKAGES/pair_sw_angle_table/table_CG_CG_CG.txt rename to examples/PACKAGES/manybody_table/table_CG_CG_CG.txt diff --git a/examples/PACKAGES/pair_sw_angle_table/README b/examples/PACKAGES/pair_sw_angle_table/README deleted file mode 100644 index 54e665ff6c..0000000000 --- a/examples/PACKAGES/pair_sw_angle_table/README +++ /dev/null @@ -1,40 +0,0 @@ -Example for pair style sw/angle/table - - -This example contains all required input files for the simulation of CG SPC/E water with -the user pair style sw/angle/table, as well as a run.sh script. - -To run the example, you have to compile LAMMPS with the MANYBODY package, including pair_sw_angle_table.h and pair_sw_angle_table.cpp. - -Running the simulation, you will reproduce results of the following publication: - -C. Scherer, and D. Andrienko, Understanding three-body contributions to coarse-grained force fields, Phys. Chem. Chem. Phys, 20(34):22387–22394, 2018, http://xlink.rsc.org/?DOI=C8CP00746B - -Here, a water molecule is represented by one coarse-grained (CG) bead. -The two-body (table_CG_CG.txt) and three-body angular (table_CG_CG_CG.txt) interaction potentials have been parametrized with force-matching (FM) with the VOTCA package (https://gitlab.mpcdf.mpg.de/votca/votca). -For more details, have a look at the publication. -For a example on the parametrization, have a look at -https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-examples/guide and -https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-examples/spce/3body_sw. - -The folder contains the LAMMPS data file (spce.data) with the starting configuration -of 1000 CG water molecules, an input file (spce.in) and a (modified) Stillinger-Weber file (spce.sw). - -The lammps input file contains the lines specifying the pair style and coefficients: - -- pair_style hybrid/overlay table linear 1200 sw/angle/table - use a combination of pair style table with 1200 linear table entries and the pair style sw/angle/table -- pair_coeff 1 1 table table_CG_CG.txt VOTCA - set the table name and keyword for the pair_style table -- pair_coeff * * sw/angle/table spce.sw type - set the name of the Stillinger-Weber file for the pair style sw/angle/table - -A hybrid pair style is used, where pair forces are calculated as a tabulated interaction (table_CG_CG.txt) and the pair style sw/angle/table is only used to calculate the three-body forces. -Therefore, in the Stillinger-Weber file all parameters refering to two-body interactions are set to zero. -As explained in the documentation of this pair style, the .sw file contains the additional lines refering to the tabulated angular potential: - -- table_CG_CG_CG.txt - file name of tabulated angular potential -- VOTCA - keyword for tabulated angular potential -- linear - angular table is of linear style -- 1001 - 1001 table entries - -The LAMMPS simulation is a standard nvt simulation. -A dump file is output with the positions and forces every 10 time steps. -You can calculate the pair distribution and compare it to the one(s) in the publicattion. diff --git a/examples/PACKAGES/pair_sw_angle_table/run.sh b/examples/PACKAGES/pair_sw_angle_table/run.sh deleted file mode 100755 index 8f64855b13..0000000000 --- a/examples/PACKAGES/pair_sw_angle_table/run.sh +++ /dev/null @@ -1,5 +0,0 @@ -#! /bin/bash -e - -#run the LAMMPS simulation (needs a current LAMMPS version compiled with the user pair_style sw/table) -lmp < spce.in > spce.out - diff --git a/examples/PACKAGES/pair_sw_angle_table/spce.data b/examples/PACKAGES/pair_sw_angle_table/spce.data deleted file mode 100644 index a56ab1b10c..0000000000 --- a/examples/PACKAGES/pair_sw_angle_table/spce.data +++ /dev/null @@ -1,1015 +0,0 @@ -Data File for CG Water - -1000 atoms -1 atom types - -0 31.0648 xlo xhi -0 31.0648 ylo yhi -0 31.0648 zlo zhi - -Masses - -1 18.0154 - -Atoms - -1 1 18.26 24.7 15.77 -2 1 12.63 1.42 27.01 -3 1 10.39 29.11 13.56 -4 1 26.47 16.64 7.23 -5 1 10.66 23.41 27.33 -6 1 19.08 3.2 21.63 -7 1 11.17 26.19 1.44 -8 1 4.61 4.04 25.72 -9 1 4.61 22.91 8.33 -10 1 30.61 22.71 25.18 -11 1 6.38 18.92 16.87 -12 1 17.83 12.53 11.09 -13 1 14.89 2.43 22.44 -14 1 28.36 30.9 26.38 -15 1 25.73 28.56 8.32 -16 1 19.61 20.22 4.43 -17 1 25.96 30.32 24.22 -18 1 14.51 17.35 16.41 -19 1 30.23 17.26 10.71 -20 1 22.68 23.23 2.3 -21 1 10.89 15.76 14.33 -22 1 1.46 20.46 12.48 -23 1 12.73 19.57 2.71 -24 1 1.21 12.02 9.88 -25 1 2.63 14.4 23.71 -26 1 16.91 20.37 4.73 -27 1 28.02 7.7 30.08 -28 1 21.22 22.47 19.66 -29 1 14.0 28.15 0.14 -30 1 19.62 19.73 1.11 -31 1 28.29 24.36 10.15 -32 1 14.05 1.1 17.64 -33 1 12.2 23.75 24.83 -34 1 24.56 26.02 13.57 -35 1 12.13 8.39 7.17 -36 1 20.47 22.28 25.02 -37 1 11.06 7.63 24.11 -38 1 6.52 22.64 30.46 -39 1 16.51 24.78 18.58 -40 1 30.18 20.56 29.19 -41 1 25.26 7.8 25.98 -42 1 20.37 4.16 3.88 -43 1 18.85 27.34 27.83 -44 1 17.72 29.84 12.78 -45 1 19.26 14.48 19.38 -46 1 29.73 4.46 4.96 -47 1 9.52 26.27 30.33 -48 1 6.55 9.25 20.32 -49 1 10.49 1.91 23.31 -50 1 17.63 1.17 14.48 -51 1 1.56 25.17 4.69 -52 1 9.08 10.39 2.29 -53 1 25.92 7.4 21.53 -54 1 25.3 5.14 28.4 -55 1 5.63 23.26 19.85 -56 1 9.6 9.85 24.85 -57 1 3.32 2.77 9.12 -58 1 28.54 15.28 22.18 -59 1 20.45 8.24 18.25 -60 1 12.86 3.73 11.61 -61 1 7.42 12.05 13.54 -62 1 1.73 28.54 25.27 -63 1 3.25 22.18 23.7 -64 1 3.27 25.38 2.24 -65 1 13.46 15.67 19.28 -66 1 31.0 6.91 13.61 -67 1 4.85 27.3 12.67 -68 1 24.48 13.52 4.98 -69 1 23.93 29.62 19.71 -70 1 5.03 13.35 19.5 -71 1 24.58 13.46 19.59 -72 1 7.42 6.82 9.03 -73 1 28.76 15.1 3.33 -74 1 12.38 17.21 6.63 -75 1 15.75 21.23 27.02 -76 1 4.58 5.06 28.19 -77 1 26.04 23.3 25.38 -78 1 30.02 7.27 9.52 -79 1 6.93 10.03 24.54 -80 1 5.61 26.93 27.34 -81 1 29.12 19.12 5.54 -82 1 18.44 27.8 14.75 -83 1 14.1 23.13 9.78 -84 1 24.12 5.55 20.72 -85 1 2.52 10.99 18.44 -86 1 1.76 6.41 21.47 -87 1 25.22 9.56 30.66 -88 1 11.87 13.25 9.12 -89 1 19.46 0.3 22.07 -90 1 28.82 12.29 11.36 -91 1 28.47 30.29 14.09 -92 1 25.51 20.94 24.33 -93 1 1.14 25.4 8.76 -94 1 1.33 27.98 3.09 -95 1 20.57 26.97 -0.04 -96 1 22.73 1.18 0.62 -97 1 19.16 16.99 30.52 -98 1 0.39 9.65 9.02 -99 1 4.41 7.21 3.22 -100 1 11.07 30.64 25.91 -101 1 7.93 25.84 26.26 -102 1 26.76 2.51 2.93 -103 1 30.8 18.15 18.49 -104 1 10.2 7.46 30.44 -105 1 4.77 20.39 26.99 -106 1 25.27 26.77 1.64 -107 1 28.51 13.99 9.33 -108 1 13.86 8.04 24.9 -109 1 30.67 29.88 23.01 -110 1 29.49 30.58 30.02 -111 1 28.74 5.08 30.95 -112 1 13.21 4.31 30.96 -113 1 5.27 3.66 5.02 -114 1 29.43 7.99 17.07 -115 1 4.19 1.37 16.63 -116 1 1.27 27.81 16.56 -117 1 30.64 5.73 25.91 -118 1 10.33 5.33 26.48 -119 1 11.56 21.77 14.77 -120 1 26.46 27.17 5.7 -121 1 14.85 25.79 8.64 -122 1 22.62 6.18 17.61 -123 1 3.45 18.53 11.84 -124 1 11.65 18.17 15.97 -125 1 23.16 17.0 1.5 -126 1 18.92 16.01 3.98 -127 1 30.05 0.25 5.23 -128 1 26.06 11.96 21.96 -129 1 16.82 2.0 10.25 -130 1 19.58 2.63 24.75 -131 1 20.09 14.75 26.62 -132 1 3.14 0.05 26.13 -133 1 4.86 11.79 12.99 -134 1 1.86 11.32 28.57 -135 1 8.82 28.6 6.22 -136 1 20.85 24.68 23.87 -137 1 7.58 25.15 3.44 -138 1 23.46 9.13 8.11 -139 1 6.45 10.24 27.37 -140 1 15.06 10.35 26.71 -141 1 13.8 18.39 26.5 -142 1 5.11 7.7 5.83 -143 1 23.27 23.16 6.67 -144 1 6.33 1.31 11.37 -145 1 14.66 22.28 21.43 -146 1 7.9 8.65 0.61 -147 1 21.83 3.67 26.17 -148 1 1.41 23.66 11.09 -149 1 10.19 17.23 22.71 -150 1 29.53 27.31 23.19 -151 1 28.69 11.38 2.33 -152 1 1.07 2.97 14.53 -153 1 23.47 30.53 14.32 -154 1 1.59 18.83 14.75 -155 1 20.38 30.6 24.38 -156 1 19.81 29.95 27.9 -157 1 12.68 27.59 26.46 -158 1 20.46 9.14 29.06 -159 1 8.69 13.98 24.71 -160 1 0.72 9.29 30.28 -161 1 11.81 20.55 12.28 -162 1 23.8 13.8 9.4 -163 1 13.63 0.51 0.95 -164 1 2.33 6.68 14.95 -165 1 15.98 6.35 25.28 -166 1 7.38 14.88 18.44 -167 1 17.07 20.48 29.16 -168 1 14.53 1.49 8.4 -169 1 28.45 1.21 20.58 -170 1 0.07 5.28 29.45 -171 1 26.0 9.98 15.37 -172 1 14.56 6.91 14.46 -173 1 20.6 9.09 23.04 -174 1 26.02 4.59 0.14 -175 1 5.21 21.9 17.55 -176 1 2.44 7.72 1.47 -177 1 1.25 30.0 13.48 -178 1 27.27 23.13 14.61 -179 1 24.04 15.61 21.64 -180 1 25.13 5.24 17.43 -181 1 4.2 15.98 12.34 -182 1 26.92 13.54 12.87 -183 1 3.38 19.38 9.08 -184 1 27.75 25.03 2.15 -185 1 26.13 20.68 16.54 -186 1 8.3 14.6 13.49 -187 1 3.04 22.87 29.93 -188 1 9.5 26.41 21.23 -189 1 6.53 2.16 2.75 -190 1 6.37 29.04 2.63 -191 1 26.58 4.38 19.69 -192 1 28.44 6.56 14.66 -193 1 25.55 11.1 28.03 -194 1 25.5 18.39 28.73 -195 1 27.67 23.47 5.65 -196 1 13.69 14.81 16.17 -197 1 22.97 27.61 24.11 -198 1 2.06 18.58 30.22 -199 1 2.07 7.13 29.2 -200 1 13.0 7.26 17.76 -201 1 10.04 16.22 30.62 -202 1 6.54 9.8 17.47 -203 1 5.65 12.68 0.64 -204 1 20.84 20.25 23.02 -205 1 22.48 27.63 21.48 -206 1 15.61 22.73 5.36 -207 1 3.52 30.36 6.24 -208 1 6.38 17.25 26.36 -209 1 14.13 10.57 22.63 -210 1 10.22 25.11 3.64 -211 1 16.63 14.7 25.08 -212 1 3.51 29.69 2.76 -213 1 19.2 11.9 21.44 -214 1 30.8 23.85 14.75 -215 1 21.02 14.34 12.4 -216 1 2.75 22.13 27.29 -217 1 29.27 14.29 6.8 -218 1 8.44 20.67 5.23 -219 1 9.42 20.06 22.95 -220 1 30.83 10.64 19.73 -221 1 19.33 14.14 8.94 -222 1 14.18 11.32 18.19 -223 1 26.55 2.39 28.55 -224 1 6.83 16.57 8.9 -225 1 13.98 8.79 1.97 -226 1 4.94 3.0 23.16 -227 1 25.39 29.46 0.63 -228 1 15.32 16.43 2.45 -229 1 5.26 29.73 29.87 -230 1 26.92 14.84 19.93 -231 1 11.87 30.08 4.52 -232 1 7.17 6.71 2.23 -233 1 10.46 1.13 18.11 -234 1 28.59 20.57 25.68 -235 1 26.54 4.84 8.44 -236 1 16.46 18.37 26.15 -237 1 30.53 0.74 15.31 -238 1 27.25 6.31 27.09 -239 1 22.42 1.65 3.87 -240 1 17.85 3.77 8.02 -241 1 11.82 8.23 11.15 -242 1 8.62 27.66 15.87 -243 1 25.19 1.89 18.37 -244 1 14.0 21.96 30.21 -245 1 29.3 1.73 28.29 -246 1 9.35 24.02 12.03 -247 1 1.05 21.5 0.35 -248 1 21.87 20.54 2.54 -249 1 10.59 15.98 17.51 -250 1 22.76 6.0 9.32 -251 1 0.31 9.13 11.87 -252 1 29.16 25.13 18.29 -253 1 1.23 29.08 7.75 -254 1 30.01 28.49 26.21 -255 1 1.87 5.92 5.03 -256 1 1.15 10.27 22.35 -257 1 11.83 10.31 5.16 -258 1 20.89 8.28 8.14 -259 1 13.48 11.78 28.37 -260 1 6.82 10.48 10.25 -261 1 7.34 4.49 18.73 -262 1 5.49 22.37 14.23 -263 1 12.31 21.05 27.47 -264 1 24.09 17.4 8.65 -265 1 22.03 11.54 20.98 -266 1 16.68 13.17 0.68 -267 1 5.52 1.47 8.78 -268 1 14.95 11.83 7.95 -269 1 5.9 10.66 7.12 -270 1 10.06 11.28 30.73 -271 1 17.72 10.71 27.46 -272 1 13.6 6.23 10.82 -273 1 23.42 30.72 9.31 -274 1 23.27 4.25 3.8 -275 1 13.79 8.37 21.07 -276 1 5.01 30.13 12.61 -277 1 26.04 24.45 17.25 -278 1 22.59 14.31 0.81 -279 1 23.74 10.37 17.17 -280 1 23.4 8.52 12.55 -281 1 10.53 23.97 21.96 -282 1 0.69 13.92 28.42 -283 1 6.94 6.27 15.01 -284 1 29.8 20.92 3.41 -285 1 10.19 20.68 19.0 -286 1 26.38 25.4 28.89 -287 1 12.34 26.9 8.27 -288 1 15.0 7.69 6.4 -289 1 24.75 13.1 2.24 -290 1 4.5 20.58 6.78 -291 1 23.27 18.25 11.48 -292 1 25.92 26.39 22.66 -293 1 24.63 4.21 6.52 -294 1 16.68 15.05 15.6 -295 1 26.39 16.17 29.89 -296 1 10.12 6.21 8.63 -297 1 14.41 14.67 12.23 -298 1 19.59 3.47 1.47 -299 1 28.21 22.43 18.25 -300 1 27.87 29.74 11.47 -301 1 22.53 24.1 13.94 -302 1 12.55 1.58 29.82 -303 1 17.45 21.28 8.34 -304 1 16.3 10.75 16.22 -305 1 16.34 13.25 17.65 -306 1 8.44 4.52 0.93 -307 1 17.47 23.79 2.3 -308 1 29.04 26.8 5.13 -309 1 13.13 11.34 24.9 -310 1 24.33 13.0 13.32 -311 1 8.21 29.74 24.23 -312 1 21.79 28.0 5.85 -313 1 13.74 20.08 10.26 -314 1 20.92 24.38 6.01 -315 1 9.83 29.56 17.99 -316 1 26.66 30.76 2.95 -317 1 24.34 3.08 1.67 -318 1 28.09 10.69 23.33 -319 1 7.08 25.28 0.77 -320 1 15.34 1.12 29.82 -321 1 26.07 12.55 7.74 -322 1 16.85 0.81 21.24 -323 1 9.96 0.57 6.36 -324 1 29.4 2.54 1.18 -325 1 5.81 1.0 5.42 -326 1 25.16 24.89 11.15 -327 1 15.43 24.93 13.71 -328 1 24.6 10.06 10.58 -329 1 20.4 12.04 15.51 -330 1 15.72 18.9 0.21 -331 1 16.5 17.21 28.81 -332 1 16.79 3.11 12.74 -333 1 22.75 6.22 6.6 -334 1 8.09 19.86 30.92 -335 1 24.15 8.75 23.65 -336 1 12.24 30.51 15.39 -337 1 8.15 26.8 18.69 -338 1 0.1 15.0 15.49 -339 1 29.84 15.71 30.0 -340 1 15.39 18.25 11.17 -341 1 1.2 15.49 18.8 -342 1 27.55 9.81 17.9 -343 1 18.93 8.9 10.06 -344 1 28.35 12.36 4.82 -345 1 11.21 13.71 30.62 -346 1 2.5 16.67 16.33 -347 1 0.47 4.2 6.99 -348 1 23.72 4.38 12.28 -349 1 16.59 3.54 16.9 -350 1 17.31 17.81 15.8 -351 1 11.58 0.3 21.21 -352 1 23.67 21.91 15.84 -353 1 7.74 2.78 23.52 -354 1 14.34 9.65 4.52 -355 1 23.35 10.88 14.55 -356 1 3.51 10.03 20.99 -357 1 14.63 21.34 1.75 -358 1 24.37 8.39 2.96 -359 1 14.8 15.5 30.48 -360 1 2.59 1.32 12.76 -361 1 0.16 13.81 25.49 -362 1 11.26 10.11 27.84 -363 1 27.8 18.65 15.07 -364 1 5.07 5.43 21.33 -365 1 14.06 5.26 19.67 -366 1 3.76 18.23 19.36 -367 1 26.68 27.25 10.67 -368 1 7.72 19.58 13.64 -369 1 29.48 16.94 16.45 -370 1 28.18 13.38 30.28 -371 1 29.97 10.41 16.17 -372 1 11.97 28.73 29.31 -373 1 14.88 0.79 25.43 -374 1 8.98 23.85 7.66 -375 1 4.78 8.21 9.79 -376 1 21.74 20.61 28.64 -377 1 20.36 18.75 17.92 -378 1 12.61 21.65 23.18 -379 1 6.36 29.76 8.49 -380 1 12.51 26.69 18.69 -381 1 22.2 17.41 6.86 -382 1 11.7 6.53 21.66 -383 1 4.62 16.22 3.24 -384 1 0.76 13.73 0.83 -385 1 21.91 13.43 5.67 -386 1 17.36 6.16 4.12 -387 1 0.34 28.1 11.89 -388 1 2.43 26.92 20.47 -389 1 0.99 22.41 4.14 -390 1 23.77 24.66 24.16 -391 1 22.41 7.79 20.57 -392 1 16.4 22.82 23.46 -393 1 24.68 28.28 17.44 -394 1 14.99 26.21 27.12 -395 1 0.75 13.41 7.7 -396 1 16.43 5.69 21.09 -397 1 19.5 6.71 27.89 -398 1 14.32 17.4 22.9 -399 1 29.04 27.81 19.17 -400 1 9.52 19.68 10.69 -401 1 5.33 27.17 17.3 -402 1 5.2 12.64 9.11 -403 1 9.8 6.14 19.74 -404 1 9.86 22.71 1.2 -405 1 0.84 12.31 14.9 -406 1 18.79 12.07 17.76 -407 1 27.21 25.79 14.27 -408 1 6.11 1.01 19.83 -409 1 8.44 5.68 12.85 -410 1 22.42 26.4 1.81 -411 1 24.0 20.11 18.63 -412 1 2.32 26.11 12.18 -413 1 26.06 7.28 15.77 -414 1 9.96 9.13 19.49 -415 1 10.74 12.01 25.79 -416 1 30.39 1.07 11.77 -417 1 9.49 20.19 26.63 -418 1 15.99 30.59 6.78 -419 1 11.0 30.74 0.96 -420 1 23.67 30.14 22.75 -421 1 24.14 9.9 19.82 -422 1 5.88 5.5 7.25 -423 1 3.45 10.72 9.52 -424 1 11.78 25.26 29.31 -425 1 15.95 27.28 17.71 -426 1 17.99 16.5 8.95 -427 1 28.47 0.47 23.29 -428 1 14.06 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7.7 -850 1 10.35 6.44 17.04 -851 1 27.27 28.95 29.77 -852 1 7.71 19.32 24.95 -853 1 23.11 17.51 14.39 -854 1 25.37 14.39 26.26 -855 1 4.73 3.99 17.92 -856 1 28.53 17.74 8.3 -857 1 28.99 9.49 7.65 -858 1 11.37 3.77 18.66 -859 1 11.01 23.57 6.0 -860 1 7.29 17.47 30.27 -861 1 18.92 10.24 0.36 -862 1 22.76 24.44 27.3 -863 1 14.27 13.05 5.04 -864 1 3.42 14.59 30.9 -865 1 9.31 22.34 24.75 -866 1 25.78 16.96 15.63 -867 1 7.18 22.01 12.25 -868 1 5.0 18.29 28.57 -869 1 23.36 20.87 22.7 -870 1 13.16 10.8 10.17 -871 1 6.42 24.78 7.47 -872 1 28.86 3.89 20.92 -873 1 4.8 3.05 13.07 -874 1 27.07 3.53 5.63 -875 1 13.11 28.33 23.92 -876 1 14.84 13.88 20.8 -877 1 15.81 7.0 16.91 -878 1 23.41 25.39 20.56 -879 1 26.08 0.43 14.19 -880 1 6.28 17.41 19.28 -881 1 2.74 4.79 19.54 -882 1 20.98 26.42 10.11 -883 1 24.18 28.48 29.18 -884 1 12.74 29.99 12.8 -885 1 27.22 16.82 18.13 -886 1 2.08 19.98 18.27 -887 1 22.0 23.67 17.16 -888 1 17.83 3.01 29.13 -889 1 9.59 26.62 13.51 -890 1 11.48 2.18 13.45 -891 1 13.57 15.29 26.47 -892 1 1.72 0.72 9.92 -893 1 2.14 30.76 17.27 -894 1 17.9 15.88 1.47 -895 1 13.47 5.84 28.76 -896 1 8.96 22.14 21.0 -897 1 12.96 24.15 0.94 -898 1 26.13 23.25 8.89 -899 1 6.01 28.65 6.08 -900 1 22.88 20.21 6.1 -901 1 30.34 20.77 10.49 -902 1 12.19 28.16 10.6 -903 1 5.8 5.33 30.84 -904 1 29.83 26.29 15.91 -905 1 18.28 0.14 5.58 -906 1 1.91 17.34 5.88 -907 1 24.05 18.42 22.53 -908 1 10.82 21.55 3.57 -909 1 11.29 26.73 5.6 -910 1 21.34 14.41 3.22 -911 1 12.61 18.99 24.17 -912 1 25.02 18.6 25.9 -913 1 29.0 21.05 13.14 -914 1 17.72 27.28 30.27 -915 1 30.56 24.81 23.12 -916 1 17.09 20.05 24.02 -917 1 7.35 6.83 21.31 -918 1 3.39 22.32 21.05 -919 1 2.28 29.8 30.23 -920 1 5.29 25.66 14.8 -921 1 26.16 30.72 21.04 -922 1 21.63 6.32 11.68 -923 1 15.45 18.06 4.65 -924 1 5.76 28.33 24.04 -925 1 15.08 29.21 16.09 -926 1 18.76 6.14 6.94 -927 1 22.31 30.25 26.46 -928 1 18.49 22.04 30.93 -929 1 11.15 16.42 9.89 -930 1 4.34 7.98 30.25 -931 1 9.29 29.92 8.58 -932 1 22.97 27.09 8.04 -933 1 20.71 16.7 15.75 -934 1 30.36 7.49 5.24 -935 1 29.56 19.54 0.83 -936 1 30.71 14.04 20.91 -937 1 19.36 4.06 27.14 -938 1 23.41 10.8 2.14 -939 1 1.51 1.32 0.44 -940 1 8.16 14.39 1.63 -941 1 20.66 6.74 4.62 -942 1 20.78 26.26 3.85 -943 1 5.11 15.12 21.64 -944 1 12.53 20.03 17.67 -945 1 28.63 18.4 12.56 -946 1 1.95 21.69 8.08 -947 1 21.53 0.93 7.84 -948 1 2.69 22.51 17.17 -949 1 19.29 22.12 6.05 -950 1 23.68 2.14 11.01 -951 1 27.14 17.8 3.72 -952 1 2.22 14.81 3.31 -953 1 23.1 6.43 14.62 -954 1 0.22 12.59 3.57 -955 1 13.21 22.86 3.67 -956 1 13.45 2.1 20.14 -957 1 12.52 17.12 0.46 -958 1 3.07 27.45 9.03 -959 1 15.33 10.95 11.78 -960 1 0.05 4.26 9.75 -961 1 23.05 16.98 24.69 -962 1 16.15 16.28 6.51 -963 1 30.05 28.87 9.61 -964 1 6.67 29.5 16.95 -965 1 21.95 14.44 14.94 -966 1 22.58 22.47 30.33 -967 1 21.34 19.29 9.9 -968 1 29.31 21.79 20.79 -969 1 5.55 2.56 30.23 -970 1 25.88 3.17 22.22 -971 1 22.38 18.32 30.08 -972 1 6.27 19.24 8.86 -973 1 0.34 24.29 1.49 -974 1 20.49 24.13 0.25 -975 1 2.94 1.41 2.74 -976 1 24.88 25.38 7.35 -977 1 28.18 14.89 14.6 -978 1 7.84 30.36 4.39 -979 1 14.54 9.59 14.4 -980 1 27.63 12.3 15.83 -981 1 11.15 14.17 27.97 -982 1 25.27 20.88 8.35 -983 1 17.06 14.76 27.78 -984 1 3.9 14.79 15.06 -985 1 13.81 3.82 17.03 -986 1 28.55 24.1 26.15 -987 1 29.28 21.79 15.76 -988 1 15.05 30.12 27.83 -989 1 15.42 3.77 6.76 -990 1 22.65 12.12 11.24 -991 1 11.29 4.96 2.18 -992 1 2.15 7.43 7.57 -993 1 30.21 10.13 26.21 -994 1 24.42 22.18 4.42 -995 1 8.68 14.72 22.08 -996 1 23.1 6.9 27.1 -997 1 18.71 27.2 21.72 -998 1 14.12 12.7 30.76 -999 1 18.81 6.5 10.98 -1000 1 26.66 15.4 4.83 diff --git a/examples/PACKAGES/pair_sw_angle_table/spce.in b/examples/PACKAGES/pair_sw_angle_table/spce.in deleted file mode 100644 index 8b1ef719a6..0000000000 --- a/examples/PACKAGES/pair_sw_angle_table/spce.in +++ /dev/null @@ -1,45 +0,0 @@ -log none - -#SPC/E water - -units real -atom_style atomic - -read_data spce.data - -#hybrid pair style consisting of -#pair_style table to read in CG pair potential -#pair_style sw/angle/table for sw interactions with tabulated angular potential -pair_style hybrid/overlay table linear 1200 sw/angle/table - -#pair coefficients -pair_coeff 1 1 table table_CG_CG.txt VOTCA -pair_coeff * * sw/angle/table spce.sw type - -#nvt run with nose-hoover thermostat -#time coupling of 100 ts for thermostat -#target T is 300 K -fix 1 all nvt temp 300.0 300.0 200.0 - -#create initial velocities -velocity all create 300 432567 dist uniform -#remove center of mass linear momentum -velocity all zero linear - -#remove center of mass linear momentum every 1000 time steps in each cartesian direction -fix remove all momentum 1000 linear 1 1 1 - -#timestep of 2 fs -timestep 2.0 - -#print out thermodynamic info every 100 ts -thermo 100 - -#run 10000 ts -run 10000 - -#write out dump file every 10 ts for 100000 ts -dump 2 all custom 10 spce.dump id type x y z fx fy fz -run 100000 - -undump 2 diff --git a/examples/PACKAGES/pair_sw_angle_table/table_CG_CG.txt b/examples/PACKAGES/pair_sw_angle_table/table_CG_CG.txt deleted file mode 100644 index f4ccdd4b4e..0000000000 --- a/examples/PACKAGES/pair_sw_angle_table/table_CG_CG.txt +++ /dev/null @@ -1,1203 +0,0 @@ -VOTCA -N 1200 R 0.010000 12.000000 - -1 1.0000000000e-02 1.5390100510e+15 2.1517330910e+16 -2 2.0000000000e-02 1.3370836560e+15 1.8774943350e+16 -3 3.0000000000e-02 1.1616510900e+15 1.6231560530e+16 -4 4.0000000000e-02 1.0092362200e+15 1.4101892510e+16 -5 5.0000000000e-02 8.7681900090e+14 1.2251648380e+16 -6 6.0000000000e-02 7.6177563290e+14 1.0644166230e+16 -7 7.0000000000e-02 6.6182657340e+14 9.2475943770e+15 -8 8.0000000000e-02 5.7499136800e+14 8.0342602660e+15 -9 9.0000000000e-02 4.9954940840e+14 6.9801221150e+15 -10 1.0000000000e-01 4.3400583970e+14 6.0642925570e+15 -11 1.1000000000e-01 3.7706193970e+14 5.2686247630e+15 -12 1.2000000000e-01 3.2758938550e+14 4.5773528620e+15 -13 1.3000000000e-01 2.8460789650e+14 3.9767795520e+15 -14 1.4000000000e-01 2.4726581000e+14 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