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Remove Make.py reference in PyLammps examples

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Also fixes some regressions due to command syntax changes
This commit is contained in:
Richard Berger
2017-07-31 13:56:20 -06:00
parent 71553cf732
commit d3169eeab3
6 changed files with 165 additions and 1049 deletions
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3
python/examples/pylammps/.gitignore vendored
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@ -1 +1,4 @@
*.orig *.orig
*-checkpoint.ipynb
*.png
*.mp4

1005
python/examples/pylammps/dihedrals/dihedral.ipynb
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File diff suppressed because one or more lines are too long

43
python/examples/pylammps/interface_usage.ipynb
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@ -29,8 +29,7 @@
"2. Compile LAMMPS as a shared library and enable exceptions and PNG support\n", "2. Compile LAMMPS as a shared library and enable exceptions and PNG support\n",
" ```bash\n", " ```bash\n",
" cd $LAMMPS_DIR/src\n", " cd $LAMMPS_DIR/src\n",
" python Make.py -m mpi -png -s exceptions -a file\n", " make mpi mode=shlib LMP_INC=\"-DLAMMPS_PNG -DLAMMPS_EXCEPTIONS\" JPG_LIB=\"-lpng\"\n",
" make mode=shlib auto\n",
" ```\n", " ```\n",
"\n", "\n",
"3. Create a python virtualenv\n", "3. Create a python virtualenv\n",
@ -67,7 +66,9 @@
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": null, "execution_count": null,
"metadata": {}, "metadata": {
"collapsed": true
},
"outputs": [], "outputs": [],
"source": [ "source": [
"from lammps import IPyLammps" "from lammps import IPyLammps"
@ -204,7 +205,9 @@
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": null, "execution_count": null,
"metadata": {}, "metadata": {
"collapsed": true
},
"outputs": [], "outputs": [],
"source": [ "source": [
"L.variable(\"a index 2\")" "L.variable(\"a index 2\")"
@ -222,7 +225,9 @@
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": null, "execution_count": null,
"metadata": {}, "metadata": {
"collapsed": true
},
"outputs": [], "outputs": [],
"source": [ "source": [
"L.variable(\"t equal temp\")" "L.variable(\"t equal temp\")"
@ -278,7 +283,9 @@
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": null, "execution_count": null,
"metadata": {}, "metadata": {
"collapsed": true
},
"outputs": [], "outputs": [],
"source": [ "source": [
"L.variable(\"b index a b c\")" "L.variable(\"b index a b c\")"
@ -314,7 +321,9 @@
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": null, "execution_count": null,
"metadata": {}, "metadata": {
"collapsed": true
},
"outputs": [], "outputs": [],
"source": [ "source": [
"L.variable(\"i loop 10\")" "L.variable(\"i loop 10\")"
@ -467,7 +476,7 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"L.runs[0].thermo.Temp" "L.runs[0].thermo"
] ]
}, },
{ {
@ -480,12 +489,23 @@
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": null, "execution_count": null,
"metadata": {}, "metadata": {
"collapsed": true
},
"outputs": [], "outputs": [],
"source": [ "source": [
"L.write_script(\"in.output\")" "L.write_script(\"in.output\")"
] ]
}, },
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"dir(L.runs[0].thermo)"
]
},
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": null, "execution_count": null,
@ -509,9 +529,10 @@
"mimetype": "text/x-python", "mimetype": "text/x-python",
"name": "python", "name": "python",
"nbconvert_exporter": "python", "nbconvert_exporter": "python",
"pygments_lexer": "ipython3" "pygments_lexer": "ipython3",
"version": "3.6.2"
} }
}, },
"nbformat": 4, "nbformat": 4,
"nbformat_minor": 0 "nbformat_minor": 1
} }

34
python/examples/pylammps/interface_usage_bonds.ipynb
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@ -30,8 +30,7 @@
" ```bash\n", " ```bash\n",
" cd $LAMMPS_DIR/src\n", " cd $LAMMPS_DIR/src\n",
" make yes-molecule\n", " make yes-molecule\n",
" python Make.py -m mpi -png -s exceptions -a file\n", " make mpi mode=shlib LMP_INC=\"-DLAMMPS_PNG -DLAMMPS_EXCEPTIONS\" JPG_LIB=\"-lpng\"\n",
" make mode=shlib auto\n",
" ```\n", " ```\n",
"\n", "\n",
"3. Create a python virtualenv\n", "3. Create a python virtualenv\n",
@ -68,7 +67,9 @@
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": null, "execution_count": null,
"metadata": {}, "metadata": {
"collapsed": true
},
"outputs": [], "outputs": [],
"source": [ "source": [
"from lammps import IPyLammps" "from lammps import IPyLammps"
@ -123,7 +124,7 @@
"L.bond_style(\"harmonic\")\n", "L.bond_style(\"harmonic\")\n",
"L.bond_coeff(1, 10.0, 1.2)\n", "L.bond_coeff(1, 10.0, 1.2)\n",
"\n", "\n",
"L.create_bonds(\"all\", \"all\", 1, 1.0, 1.5)\n", "L.create_bonds(\"many\", \"all\", \"all\", 1, 1.0, 1.5)\n",
"\n", "\n",
"L.neighbor(0.3, \"bin\")\n", "L.neighbor(0.3, \"bin\")\n",
"L.neigh_modify(\"delay\", 0, \"every\", 1, \"check yes\")\n", "L.neigh_modify(\"delay\", 0, \"every\", 1, \"check yes\")\n",
@ -253,7 +254,9 @@
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": null, "execution_count": null,
"metadata": {}, "metadata": {
"collapsed": true
},
"outputs": [], "outputs": [],
"source": [ "source": [
"L.variable(\"a index 2\")" "L.variable(\"a index 2\")"
@ -271,7 +274,9 @@
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": null, "execution_count": null,
"metadata": {}, "metadata": {
"collapsed": true
},
"outputs": [], "outputs": [],
"source": [ "source": [
"L.variable(\"t equal temp\")" "L.variable(\"t equal temp\")"
@ -327,7 +332,9 @@
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": null, "execution_count": null,
"metadata": {}, "metadata": {
"collapsed": true
},
"outputs": [], "outputs": [],
"source": [ "source": [
"L.variable(\"b index a b c\")" "L.variable(\"b index a b c\")"
@ -363,7 +370,9 @@
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": null, "execution_count": null,
"metadata": {}, "metadata": {
"collapsed": true
},
"outputs": [], "outputs": [],
"source": [ "source": [
"L.variable(\"i loop 10\")" "L.variable(\"i loop 10\")"
@ -470,7 +479,9 @@
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": null, "execution_count": null,
"metadata": {}, "metadata": {
"collapsed": true
},
"outputs": [], "outputs": [],
"source": [] "source": []
} }
@ -490,9 +501,10 @@
"mimetype": "text/x-python", "mimetype": "text/x-python",
"name": "python", "name": "python",
"nbconvert_exporter": "python", "nbconvert_exporter": "python",
"pygments_lexer": "ipython3" "pygments_lexer": "ipython3",
"version": "3.6.2"
} }
}, },
"nbformat": 4, "nbformat": 4,
"nbformat_minor": 0 "nbformat_minor": 1
} }

117
python/examples/pylammps/montecarlo/mc.ipynb
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12
python/examples/pylammps/simple.ipynb
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@ -29,8 +29,7 @@
"2. Compile LAMMPS as a shared library and enable exceptions and PNG support\n", "2. Compile LAMMPS as a shared library and enable exceptions and PNG support\n",
" ```bash\n", " ```bash\n",
" cd $LAMMPS_DIR/src\n", " cd $LAMMPS_DIR/src\n",
" python Make.py -m mpi -png -s exceptions -a file\n", " make mpi mode=shlib LMP_INC=\"-DLAMMPS_PNG -DLAMMPS_EXCEPTIONS\" JPG_LIB=\"-lpng\"\n",
" make mode=shlib auto\n",
" ```\n", " ```\n",
"\n", "\n",
"3. Create a python virtualenv\n", "3. Create a python virtualenv\n",
@ -67,7 +66,9 @@
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": null, "execution_count": null,
"metadata": {}, "metadata": {
"collapsed": true
},
"outputs": [], "outputs": [],
"source": [ "source": [
"from lammps import IPyLammps" "from lammps import IPyLammps"
@ -144,9 +145,10 @@
"mimetype": "text/x-python", "mimetype": "text/x-python",
"name": "python", "name": "python",
"nbconvert_exporter": "python", "nbconvert_exporter": "python",
"pygments_lexer": "ipython3" "pygments_lexer": "ipython3",
"version": "3.6.2"
} }
}, },
"nbformat": 4, "nbformat": 4,
"nbformat_minor": 0 "nbformat_minor": 1
} }