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