Try_and_Learn_2.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "0d4f16d9-5ff7-4a32-8942-0f77a1b9a3b8",
   "metadata": {},
   "outputs": [],
   "source": [
    "#from selm_lammps.lammps import IPyLammps\n",
    "#L=IPyLammps();\n",
    "\n",
    "import numpy as np"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "feda80a1-1bdf-479c-a270-689d602d9006",
   "metadata": {},
   "outputs": [],
   "source": [
    "s=\"\"\"\n",
    "atom_style\tatomic\n",
    "neighbor\t0.3 bin\n",
    "neigh_modify\tdelay 5\n",
    "\n",
    "# create geometry\n",
    "\n",
    "lattice\t\tfcc 3.52\n",
    "region\t\tbox block 0 100 0 100 0 100\n",
    "create_box\t3 box\n",
    "create_atoms\t1 box\n",
    "\n",
    "region 1 block INF INF INF 1.25 INF INF\n",
    "group lower_y region 1\n",
    "region 2 block INF 1.25 INF INF  INF INF\n",
    "group lower_x region 2\n",
    "region 3 block INF  INF INF  INF INF -200\n",
    "group lower_z region 3\n",
    "region 4 block INF INF 99 INF  INF INF\n",
    "group upper_y region 4\n",
    "region 5 block 99 INF INF INF  INF INF\n",
    "group upper_x region 5\n",
    "region 6 block INF  INF INF  INF 99 INF\n",
    "group upper_z region 6\n",
    "\n",
    "group boundary union lower_y lower_x lower_z upper_y upper_x upper_z\n",
    "group flow subtract all boundary\n",
    "\"\"\"\n",
    "\n",
    "for line in s.splitlines():\n",
    " # print_log(line);\n",
    "  L.command(line);"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "764ffc17-12b8-4c9b-a005-bf2cc983f46a",
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "x=np.random.uniform(3,97,10)\n",
    "y=np.random.uniform(3,97,10)\n",
    "z=np.random.uniform(3,97,10)\n",
    "\n",
    "points=list(zip(x,y,z))\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "1f81ae20-cede-4300-a091-303f51c7d7bc",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[(95.46829618878418, 76.06680227899967, 44.117367175177954),\n",
       " (37.15227160956565, 86.4304014532849, 77.98575225092368),\n",
       " (3.9566584532075204, 56.2107099760403, 37.6594933028452),\n",
       " (74.10999246553853, 74.09991010658874, 6.954853361445133),\n",
       " (40.860274592805325, 37.96750746027811, 15.498694599830284),\n",
       " (30.381627449201645, 61.818968743167076, 6.895953216017736),\n",
       " (33.79401867186104, 62.34283634624712, 34.492406314593204),\n",
       " (59.28855157673209, 4.03360481004575, 38.81392862059011),\n",
       " (33.44337648250786, 52.41537263012225, 24.87877899867956),\n",
       " (87.86571054637172, 36.21406176896551, 21.361635138785584)]"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "points"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "dfe0eb25-2e66-47b5-9382-a2d4f7409b2c",
   "metadata": {},
   "outputs": [],
   "source": [
    "j=1\n",
    "for i in points:\n",
    "    L.region(j,\"sphere\",i[0],i[1],i[2],3)\n",
    "    j=j+1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "11bcc2ba-5015-472e-a2dc-5a2348c69a9e",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "LAMMPS (29 Oct 2020)\n",
      "Lattice spacing in x,y,z = 1.0435320 1.0435320 1.0435320\n",
      "Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (104.35320 104.35320 104.35320)\n",
      "  1 by 1 by 1 MPI processor grid\n",
      "Created 4000000 atoms\n",
      "  create_atoms CPU = 0.847 seconds\n",
      "WARNING: Ignoring unknown or incorrect info command flag (../info.cpp:257)\n",
      "\n",
      "Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info\n",
      "Printed on Sat Dec 23 22:20:06 2023\n",
      "\n",
      "\n",
      "LAMMPS version: 29 Oct 2020 / 20201029\n",
      "\n",
      "OS information: Linux 6.2.0-37-generic on x86_64\n",
      "\n",
      "sizeof(smallint): 32-bit\n",
      "sizeof(imageint): 32-bit\n",
      "sizeof(tagint):   32-bit\n",
      "sizeof(bigint):   64-bit\n",
      "\n",
      "Compiler: GNU C++ 6.3.0 20170516 with OpenMP not enabled\n",
      "C++ standard: C++14\n",
      "\n",
      "Active compile time flags:\n",
      "\n",
      "-DLAMMPS_GZIP\n",
      "-DLAMMPS_PNG\n",
      "-DLAMMPS_JPEG\n",
      "-DLAMMPS_FFMPEG\n",
      "-DLAMMPS_EXCEPTIONS\n",
      "-DLAMMPS_SMALLBIG\n",
      "\n",
      "Installed packages:\n",
      "\n",
      "MOLECULE USER-MISC USER-VTK \n",
      "\n",
      "Memory allocation information (MPI rank 0):\n",
      "\n",
      "Total dynamically allocated memory: 428.8 Mbyte\n",
      "Current reserved memory pool size: 445.1 Mbyte\n",
      "Maximum resident set size: 424.0 Mbyte\n",
      "\n",
      "Communication information:\n",
      "MPI library level: MPI v1.2\n",
      "MPI version: LAMMPS MPI STUBS for LAMMPS version 29 Oct 2020\n",
      "Comm style = brick,  Comm layout = uniform\n",
      "Communicate velocities for ghost atoms = no\n",
      "Communication mode = single\n",
      "Communication cutoff = 0.0\n",
      "Nprocs = 1,   Nthreads = 1\n",
      "Processor grid = 1 x 1 x 1\n",
      "\n",
      "System information:\n",
      "Units         = lj\n",
      "Atom style    = atomic\n",
      "Atom map      = none\n",
      "Atoms     =      4000000,  types =        3,  style = none\n",
      "Kspace style = none\n",
      "\n",
      "Dimensions = 3\n",
      "Orthogonal box = 104.35320 x 104.35320 x 104.35320\n",
      "Boundaries = p,p p,p p,p\n",
      "xlo, xhi = 0.0000000, 104.35320\n",
      "ylo, yhi = 0.0000000, 104.35320\n",
      "zlo, zhi = 0.0000000, 104.35320\n",
      "\n",
      "Coeff status information:\n",
      "\n",
      "Group information:\n",
      "Group[ 0]:     all              (static)\n",
      "\n",
      "Region information:\n",
      "Region[  0]:  box,              style = block,            side = in\n",
      "   Boundary:  lo 0.0000000 0.0000000 0.0000000  hi 104.35320 104.35320 104.35320\n",
      "Region[  1]:  1,                style = sphere,           side = in\n",
      "   Boundary:  lo 58.658590 37.333949 92.892644  hi 64.919782 43.595142 99.153836\n",
      "Region[  2]:  2,                style = sphere,           side = in\n",
      "   Boundary:  lo 85.680052 92.089389 4.7081725  hi 91.941244 98.350581 10.969365\n",
      "Region[  3]:  3,                style = sphere,           side = in\n",
      "   Boundary:  lo 29.624455 18.924091 62.571878  hi 35.885648 25.185283 68.833070\n",
      "Region[  4]:  4,                style = sphere,           side = in\n",
      "   Boundary:  lo 9.4001962 17.704231 75.674472  hi 15.661388 23.965423 81.935664\n",
      "Region[  5]:  5,                style = sphere,           side = in\n",
      "   Boundary:  lo 11.215979 68.859748 25.613167  hi 17.477172 75.120940 31.874359\n",
      "Region[  6]:  6,                style = sphere,           side = in\n",
      "   Boundary:  lo 50.492744 35.463820 62.999267  hi 56.753936 41.725012 69.260459\n",
      "Region[  7]:  7,                style = sphere,           side = in\n",
      "   Boundary:  lo 1.6684049 56.621592 30.237028  hi 7.9295970 62.882784 36.498220\n",
      "Region[  8]:  8,                style = sphere,           side = in\n",
      "   Boundary:  lo 79.149263 80.095579 42.509612  hi 85.410455 86.356771 48.770804\n",
      "Region[  9]:  9,                style = sphere,           side = in\n",
      "   Boundary:  lo 86.220244 6.6991802 55.706444  hi 92.481436 12.960372 61.967636\n",
      "Region[ 10]:  10,               style = sphere,           side = in\n",
      "   Boundary:  lo 45.946218 76.984768 11.303348  hi 52.207410 83.245960 17.564540\n",
      "\n",
      "Compute information:\n",
      "Compute[  0]:  thermo_temp,      style = temp,             group = all\n",
      "Compute[  1]:  thermo_press,     style = pressure,         group = all\n",
      "Compute[  2]:  thermo_pe,        style = pe,               group = all\n",
      "\n",
      "Dump information:\n",
      "\n",
      "Fix information:\n",
      "\n",
      "Variable information:\n",
      "\n",
      "Total time information (MPI rank 0):\n",
      "  CPU time:    0:00:02\n",
      " Wall time:    0:00:17\n",
      "\n",
      "Styles information:\n",
      "\n",
      "Atom styles:\n",
      "\n",
      "angle           atomic          body            bond            charge          \n",
      "ellipsoid       full            hybrid          line            molecular       \n",
      "sphere          template        tri             \n",
      "\n",
      "\n",
      "\n",
      "Integrate styles:\n",
      "\n",
      "respa           verlet          \n",
      "\n",
      "\n",
      "\n",
      "Minimize styles:\n",
      "\n",
      "cg              fire            fire/old        hftn            quickmin        \n",
      "sd              \n",
      "\n",
      "\n",
      "\n",
      "Pair styles:\n",
      "\n",
      "agni            beck            born            born/coul/dsf   born/coul/wolf  \n",
      "buck            buck/coul/cut   buck/mdf        cosine/squared  coul/cut        \n",
      "coul/debye      coul/diel       coul/dsf        coul/shield     coul/slater/cut \n",
      "coul/slater/long                coul/streitz    coul/wolf       dpd             \n",
      "dpd/tstat       drip            e3b             edip            edip/multi      \n",
      "extep           gauss           gauss/cut       hbond/dreiding/lj               \n",
      "hbond/dreiding/morse            hybrid          hybrid/overlay  ilp/graphene/hbn                \n",
      "kolmogorov/crespi/full          kolmogorov/crespi/z             lebedeva/z      \n",
      "lennard/mdf     list            lj/charmm/coul/charmm           \n",
      "lj/charmm/coul/charmm/implicit  lj/charmmfsw/coul/charmmfsh     lj/cubic        \n",
      "lj/cut          lj/cut/coul/cut lj/cut/coul/debye               lj/cut/coul/dsf \n",
      "lj/cut/coul/wolf                lj/cut/tip4p/cut                lj/expand       \n",
      "lj/expand/coul/long             lj/gromacs      lj/gromacs/coul/gromacs         \n",
      "lj/mdf          lj/sf           lj/sf/dipole/sf lj/smooth       lj/smooth/linear                \n",
      "lj96/cut        local/density   meam/spline     meam/sw/spline  mie/cut         \n",
      "momb            morse           morse/smooth/linear             reax            \n",
      "soft            srp             table           tersoff/table   tip4p/cut       \n",
      "ufm             yukawa          zbl             zero            \n",
      "\n",
      "\n",
      "\n",
      "Bond styles:\n",
      "\n",
      "fene            fene/expand     gromos          harmonic        harmonic/shift  \n",
      "harmonic/shift/cut              hybrid          morse           nonlinear       \n",
      "quartic         special         table           zero            \n",
      "\n",
      "\n",
      "\n",
      "Angle styles:\n",
      "\n",
      "charmm          cosine          cosine/delta    cosine/periodic cosine/shift    \n",
      "cosine/shift/exp                cosine/squared  dipole          fourier         \n",
      "fourier/simple  harmonic        hybrid          quartic         table           \n",
      "zero            \n",
      "\n",
      "\n",
      "\n",
      "Dihedral styles:\n",
      "\n",
      "charmm          charmmfsw       cosine/shift/exp                fourier         \n",
      "harmonic        helix           hybrid          multi/harmonic  nharmonic       \n",
      "opls            quadratic       spherical       table           table/cut       \n",
      "zero            \n",
      "\n",
      "\n",
      "\n",
      "Improper styles:\n",
      "\n",
      "cossq           cvff            distance        fourier         harmonic        \n",
      "hybrid          ring            umbrella        zero            \n",
      "\n",
      "\n",
      "\n",
      "KSpace styles:\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "Fix styles:\n",
      "\n",
      "accelerate/cos  adapt           addforce        addtorque       ave/atom        \n",
      "ave/chunk       ave/correlate   ave/correlate/long              ave/histo       \n",
      "ave/histo/weight                ave/spatial     ave/spatial/sphere              \n",
      "ave/time        aveforce        balance         box/relax       cmap            \n",
      "controller      deform          drag            dt/reset        \n",
      "electron/stopping               enforce2d       external        ffl             \n",
      "filter/corotate flow/gauss      gle             gravity         grem            \n",
      "halt            heat            imd             indent          ipi             \n",
      "langevin        lineforce       momentum        momentum/chunk  move            \n",
      "nph             nph/sphere      npt             npt/cauchy      npt/sphere      \n",
      "numdiff         nve             nve/limit       nve/noforce     nve/sphere      \n",
      "nvk             nvt             nvt/sllod       nvt/sphere      orient/eco      \n",
      "pafi            pimd            planeforce      press/berendsen print           \n",
      "propel/self     property/atom   recenter        restrain        rhok            \n",
      "selm            setforce        smd             spring          spring/chunk    \n",
      "spring/rg       spring/self     store/force     store/state     temp/berendsen  \n",
      "temp/csld       temp/csvr       temp/rescale    ti/spring       tmd             \n",
      "ttm/mod         vector          viscous         wall/ees        wall/harmonic   \n",
      "wall/l"
     ]
    }
   ],
   "source": [
    "s=\"\"\"\n",
    "info all out\n",
    "\"\"\"\n",
    "\n",
    "#print_log(\"Sending commands to LAMMPs\");\n",
    "for line in s.splitlines():\n",
    " # print_log(line);\n",
    "  L.command(line);"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "4471e25c",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "7\n",
      "8\n",
      "9\n",
      "10\n",
      "11\n",
      "12\n",
      "13\n",
      "14\n",
      "15\n",
      "16\n"
     ]
    }
   ],
   "source": [
    "for j in range(7,17):\n",
    "    print(j)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "62ad0818",
   "metadata": {},
   "outputs": [],
   "source": [
    "original=\"delete_atoms region \"\n",
    "for j in range(1,11):\n",
    "    line1=original+str(j)\n",
    "    line2=\"fix \"+ str(j+1) +\"flow indent \"+str(100)+\" sphere \"+ str(points[j-1][0])+\" \"+str(points[j-1][1])+\" \"+str(points[j-1][2])+\" \"+str(4)\n",
    "    L.command(line)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "0e77249f-bf7d-4036-9909-a12edc1ad6f7",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "j1043     wall/lj126      wall/lj93       wall/morse      wall/reflect    \n",
      "wall/reflect/stochastic         wall/region     wall/region/ees \n",
      "\n",
      "\n",
      "\n",
      "Compute styles:\n",
      "\n",
      "ackland/atom    adf             aggregate/atom  angle           angle/local     \n",
      "angmom/chunk    basal/atom      bond            bond/local      centro/atom     \n",
      "centroid/stress/atom            chunk/atom      chunk/spread/atom               \n",
      "cluster/atom    cna/atom        cnp/atom        com             com/chunk       \n",
      "contact/atom    coord/atom      dihedral        dihedral/local  dipole/chunk    \n",
      "displace/atom   entropy/atom    erotate/sphere  erotate/sphere/atom             \n",
      "fragment/atom   global/atom     group/group     gyration        gyration/chunk  \n",
      "gyration/shape  gyration/shape/chunk            heat/flux       hexorder/atom   \n",
      "hma             improper        improper/local  inertia/chunk   ke              \n",
      "ke/atom         momentum        msd             msd/chunk       omega/chunk     \n",
      "orientorder/atom                pair            pair/local      pe              \n",
      "pe/atom         pressure        pressure/cylinder               property/atom   \n",
      "property/chunk  property/local  rdf             reduce          reduce/chunk    \n",
      "reduce/region   slice           stress/atom     stress/mop      \n",
      "stress/mop/profile              stress/mop_selm stress/mop_selm/profile         \n",
      "temp            temp/chunk      temp/com        temp/deform     temp/partial    \n",
      "temp/profile    temp/ramp       temp/region     temp/rotate     temp/sphere     \n",
      "torque/chunk    vacf            vcm/chunk       viscosity/cos   \n",
      "\n",
      "\n",
      "\n",
      "Region styles:\n",
      "\n",
      "block           cone            cylinder        intersect       plane           \n",
      "prism           sphere          union           \n",
      "\n",
      "\n",
      "\n",
      "Dump styles:\n",
      "\n",
      "atom            cfg             custom          dcd             image           \n",
      "local           movie           vtk             xyz             \n",
      "\n",
      "\n",
      "\n",
      "Command styles (add-on input script commands):\n",
      "\n",
      "balance         change_box      create_atoms    create_bonds    create_box      \n",
      "delete_atoms    delete_bonds    displace_atoms  info            minimize        \n",
      "read_data       read_dump       read_restart    replicate       rerun           \n",
      "reset_atom_ids  reset_ids       reset_mol_ids   run             set             \n",
      "temper/grem     temper/npt      velocity        write_coeff     write_data      \n",
      "write_dump      write_restart   \n",
      "\n",
      "\n",
      "\n",
      "Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info\n",
      "\n",
      "Deleted 451 atoms, new total = 3999549\n",
      "Deleted 449 atoms, new total = 3999100\n",
      "Deleted 448 atoms, new total = 3998652\n",
      "Deleted 466 atoms, new total = 3998186\n",
      "Deleted 447 atoms, new total = 3997739\n",
      "Deleted 450 atoms, new total = 3997289\n",
      "Deleted 454 atoms, new total = 3996835\n",
      "Deleted 457 atoms, new total = 3996378\n",
      "Deleted 453 atoms, new total = 3995925\n",
      "Deleted 454 atoms, new total = 3995471\n",
      "WARNING: Ignoring unknown or incorrect info command flag (../info.cpp:257)\n",
      "\n",
      "Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info\n",
      "Printed on Sat Dec 23 22:21:24 2023\n",
      "\n",
      "\n",
      "LAMMPS version: 29 Oct 2020 / 20201029\n",
      "\n",
      "OS information: Linux 6.2.0-37-generic on x86_64\n",
      "\n",
      "sizeof(smallint): 32-bit\n",
      "sizeof(imageint): 32-bit\n",
      "sizeof(tagint):   32-bit\n",
      "sizeof(bigint):   64-bit\n",
      "\n",
      "Compiler: GNU C++ 6.3.0 20170516 with OpenMP not enabled\n",
      "C++ standard: C++14\n",
      "\n",
      "Active compile time flags:\n",
      "\n",
      "-DLAMMPS_GZIP\n",
      "-DLAMMPS_PNG\n",
      "-DLAMMPS_JPEG\n",
      "-DLAMMPS_FFMPEG\n",
      "-DLAMMPS_EXCEPTIONS\n",
      "-DLAMMPS_SMALLBIG\n",
      "\n",
      "Installed packages:\n",
      "\n",
      "MOLECULE USER-MISC USER-VTK \n",
      "\n",
      "Memory allocation information (MPI rank 0):\n",
      "\n",
      "Total dynamically allocated memory: 428.8 Mbyte\n",
      "Current reserved memory pool size: 445.2 Mbyte\n",
      "Maximum resident set size: 439.3 Mbyte\n",
      "\n",
      "Communication information:\n",
      "MPI library level: MPI v1.2\n",
      "MPI version: LAMMPS MPI STUBS for LAMMPS version 29 Oct 2020\n",
      "Comm style = brick,  Comm layout = uniform\n",
      "Communicate velocities for ghost atoms = no\n",
      "Communication mode = single\n",
      "Communication cutoff = 0.0\n",
      "Nprocs = 1,   Nthreads = 1\n",
      "Processor grid = 1 x 1 x 1\n",
      "\n",
      "System information:\n",
      "Units         = lj\n",
      "Atom style    = atomic\n",
      "Atom map      = none\n",
      "Atoms     =      3995471,  types =        3,  style = none\n",
      "Kspace style = none\n",
      "\n",
      "Dimensions = 3\n",
      "Orthogonal box = 104.35320 x 104.35320 x 104.35320\n",
      "Boundaries = p,p p,p p,p\n",
      "xlo, xhi = 0.0000000, 104.35320\n",
      "ylo, yhi = 0.0000000, 104.35320\n",
      "zlo, zhi = 0.0000000, 104.35320\n",
      "\n",
      "Coeff status information:\n",
      "\n",
      "Group information:\n",
      "Group[ 0]:     all              (static)\n",
      "\n",
      "Region information:\n",
      "Region[  0]:  box,              style = block,            side = in\n",
      "   Boundary:  lo 0.0000000 0.0000000 0.0000000  hi 104.35320 104.35320 104.35320\n",
      "Region[  1]:  1,                style = sphere,           side = in\n",
      "   Boundary:  lo 58.658590 37.333949 92.892644  hi 64.919782 43.595142 99.153836\n",
      "Region[  2]:  2,                style = sphere,           side = in\n",
      "   Boundary:  lo 85.680052 92.089389 4.7081725  hi 91.941244 98.350581 10.969365\n",
      "Region[  3]:  3,                style = sphere,           side = in\n",
      "   Boundary:  lo 29.624455 18.924091 62.571878  hi 35.885648 25.185283 68.833070\n",
      "Region[  4]:  4,                style = sphere,           side = in\n",
      "   Boundary:  lo 9.4001962 17.704231 75.674472  hi 15.661388 23.965423 81.935664\n",
      "Region[  5]:  5,                style = sphere,           side = in\n",
      "   Boundary:  lo 11.215979 68.859748 25.613167  hi 17.477172 75.120940 31.874359\n",
      "Region[  6]:  6,                style = sphere,           side = in\n",
      "   Boundary:  lo 50.492744 35.463820 62.999267  hi 56.753936 41.725012 69.260459\n",
      "Region[  7]:  7,                style = sphere,           side = in\n",
      "   Boundary:  lo 1.6684049 56.621592 30.237028  hi 7.9295970 62.882784 36.498220\n",
      "Region[  8]:  8,                style = sphere,           side = in\n",
      "   Boundary:  lo 79.149263 80.095579 42.509612  hi 85.410455 86.356771 48.770804\n",
      "Region[  9]:  9,                style = sphere,           side = in\n",
      "   Boundary:  lo 86.220244 6.6991802 55.706444  hi 92.481436 12.960372 61.967636\n",
      "Region[ 10]:  10,               style = sphere,           side = in\n",
      "   Boundary:  lo 45.946218 76.984768 11.303348  hi 52.207410 83.245960 17.564540\n",
      "\n",
      "Compute information:\n",
      "Compute[  0]:  thermo_temp,      style = temp,             group = all\n",
      "Compute[  1]:  thermo_press,     style = pressure,         group = all\n",
      "Compute[  2]:  thermo_pe,        style = pe,               group = all\n",
      "\n",
      "Dump information:\n",
      "\n",
      "Fix information:\n",
      "\n",
      "Variable information:\n",
      "\n",
      "Total time information (MPI rank 0):\n",
      "  CPU time:    0:00:04\n",
      " Wall time:    0:01:35\n",
      "\n",
      "Styles information:\n",
      "\n",
      "Atom styles:\n",
      "\n",
      "angle           atomic          body            bond            charge          \n",
      "ellipsoid       full            hybrid          line            molecular       \n",
      "sphere          template        tri             \n",
      "\n",
      "\n",
      "\n",
      "Integrate styles:\n",
      "\n",
      "respa           verlet          \n",
      "\n",
      "\n",
      "\n",
      "Minimize styles:\n",
      "\n",
      "cg              fire            fire/old        hftn            quickmin        \n",
      "sd              \n",
      "\n",
      "\n",
      "\n",
      "Pair styles:\n",
      "\n",
      "agni            beck            born            born/coul/dsf   born/coul/wolf  \n",
      "buck            buck/coul/cut   buck/mdf        cosine/squared  coul/cut        \n",
      "coul/debye      coul/diel       coul/dsf        coul/shield     coul/slater/cut \n",
      "coul/slater/long                coul/streitz    coul/wolf       dpd             \n",
      "dpd/tstat       drip            e3b             edip            edip/multi      \n",
      "extep           gauss           gauss/cut       hbond/dreiding/lj               \n",
      "hbond/dreiding/morse            hybrid          hybrid/overlay  ilp/graphene/hbn                \n",
      "kolmogorov/crespi/full          kolmogorov/crespi/z             lebedeva/z      \n",
      "lennard/mdf     list            lj/charmm/coul/charmm           \n",
      "lj/charmm/coul/charmm/implicit  lj/charmmfsw/coul/charmmfsh     lj/cubic        \n",
      "lj/cut          lj/cut/coul/cut lj/cut/coul/debye               lj/cut/coul/dsf \n",
      "lj/cut/coul/wolf                lj/cut/tip4p/cut                lj/expand       \n",
      "lj/expand/coul/long             lj/gromacs      lj/gromacs/coul/gromacs         \n",
      "lj/mdf          lj/sf           lj/sf/dipole/sf lj/smooth       lj/smooth/linear                \n",
      "lj96/cut        local/density   meam/spline     meam/sw/spline  mie/cut         \n",
      "momb            morse           morse/smooth/linear             reax            \n",
      "soft            srp             table           tersoff/table   tip4p/cut       \n",
      "ufm             yukawa          zbl             zero            \n",
      "\n",
      "\n",
      "\n",
      "Bond styles:\n",
      "\n",
      "fene            fene/expand     gromos          harmonic        harmonic/shift  \n",
      "harmonic/shift/cut              hybrid          morse           nonlinear       \n",
      "quartic         special         table           zero            \n",
      "\n",
      "\n",
      "\n",
      "Angle styles:\n",
      "\n",
      "charmm          cosine          cosine/delta    cosine/periodic cosine/shift    \n",
      "cosine/shift/exp                cosine/squared  dipole          fourier         \n",
      "fourier/simple  harmonic        hybrid          quartic         table           \n",
      "zero            \n",
      "\n",
      "\n",
      "\n",
      "Dihedral styles:\n",
      "\n",
      "charmm          charmmfsw       cosine/shift/exp                fourier         \n",
      "harmonic        helix           hybrid          multi/harmonic  nharmonic       \n",
      "opls            quadratic       spherical       table           table/cut       \n",
      "zero            \n",
      "\n",
      "\n",
      "\n",
      "Improper styles:\n",
      "\n",
      "cossq           cvff            distance        fourier         harmonic        \n",
      "hybrid          ring            umbrella        zero            \n",
      "\n",
      "\n",
      "\n",
      "KSpace styles:\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "Fix styles:\n",
      "\n",
      "accelerate/cos  adapt           addforce        addtorque       ave/atom        \n",
      "ave/chunk       ave/correlate   ave/correlate/long              ave/histo       \n",
      "ave/histo/weight                ave/spatial     ave/spatial/sphere              \n",
      "ave/time        aveforce        balance         box/relax       cmap            \n",
      "controller      deform          drag            dt/reset        \n",
      "electron/stopping               enforce2d       external        ffl             \n",
      "filter/corotate flow/gauss      gle             gravity         grem            \n",
      "halt            heat            imd             indent          ipi             \n",
      "langevin        lineforce       momentum        momentum/chunk  move            \n",
      "nph             nph/sphere      npt             npt/cauchy      npt/sphere      \n",
      "numdiff         nve             nve/limit       nve/noforce     nve/sphere      \n",
      "nvk             nvt             nvt/sllod       nvt/sphere      orient/eco      \n",
      "pafi            pimd            planeforce      press/berendsen print           \n",
      "propel/self     property/atom   recenter        restrain        rhok            \n",
      "selm            setforce        smd             spring          spring/chunk    \n",
      "spring/rg       spring/self     store/force     store/state     temp/berendsen  \n",
      "temp/csld       temp/csvr       temp/rescale    ti/spring       tmd             \n",
      "ttm/mod         vector          viscous         wall/ees        wall/harmonic   \n",
      "wall/lj1043     wall/lj126      wall/lj93       wall/morse      wall/reflect    \n",
      "wall/reflect/stochastic         wall/region     wall/region/ees \n",
      "\n",
      "\n",
      "\n",
      "Compute styles:\n",
      "\n",
      "ackland/atom    adf             aggregate/atom  angle           angle/local     \n",
      "angmom/chunk    basal/atom      bond            bond/local      centro/atom     \n",
      "centroid/stress/atom            chunk/atom      chunk/spread/atom               \n",
      "cluster/atom    cna/atom        cnp/atom        com             com/chunk       \n",
      "contact/atom    coord/atom      dihedral        dihedral/local  dipole/chunk    \n",
      "displace/atom   entropy/atom    erotate/sphere  erotate/sphere/atom             \n",
      "fragment/atom   global/atom     group/group     gyration        gyration/chunk  \n",
      "gyration/shape  gyration/shape/chunk            heat/flux       hexorder/atom   \n",
      "hma             improper        improper/local  inertia/chunk   ke              \n",
      "ke/atom         momentum        msd             msd/chunk       omega/chunk     \n",
      "orientorder/atom                pair            pair/local      pe              \n",
      "pe/atom         pressure        pressure/cylinder               property/atom   \n",
      "property/chunk  property/local  rdf             reduce          reduce/chunk    \n",
      "reduce/region   slice           stress/atom     stress/mop      \n",
      "stress/mop/profile              stress/mop_selm stress/mop_selm/profile         \n",
      "temp            temp/chunk      temp/com        temp/deform     temp/partial    \n",
      "temp/profile    temp/ramp       temp/region     temp/rotate     temp/sphere     "
     ]
    }
   ],
   "source": [
    "s=\"\"\"\n",
    "info all out\n",
    "\"\"\"\n",
    "\n",
    "#print_log(\"Sending commands to LAMMPs\");\n",
    "for line in s.splitlines():\n",
    " # print_log(line);\n",
    "  L.command(line);"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "751e6a59-e390-45d3-96e0-0db62241c33b",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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