Commit 946032e2 authored by Anastasia's avatar Anastasia
Browse files

draft for the test added

parent a1784bfb
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"# Basic imports\n",
"%matplotlib inline\n",
"import openpathsampling as paths\n",
"import numpy as np\n"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"# here is a 2D potential:\n",
"# V = 1/6 * (4 * (1 - x^2 - y^2)^2 + 2 * (x^2 - 2)^2 + ((x + y)^2 - 1)^2 + ((x - y)^2 - 1)^2 - 2)N\n",
"class NEWPR(paths.engines.toy.PES):\n",
" '''\n",
" Simple 2D-potential \n",
" \n",
" '''\n",
" pass\n",
"\n",
"my_pes=1"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"<__main__.NEWPR at 0x7f00acceb190>"
]
},
"execution_count": 13,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"NEWPR()"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"# Is `import toys.something` always needed???? \n",
"topology# = particle (m=1)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"integ# = Langevin integrator, friction gamma = 0.25\n",
"options={\n",
" 'integ' : integ,\n",
" 'n_frames_max' : 10,\n",
" 'n_steps_per_frame' : 1\n",
"}"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"engine '''NOT TOY!!! I guesss= toys.Engine(\n",
" options=options,\n",
" topology=topology\n",
")'''"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Object `paths.engines.openmmp` not found.\n"
]
}
],
"source": [
"stateA = 1# = circle(center = (0, -1), radius = 0.2)\n",
"stateB = 1 # = circle(center = (0, 1), radius = 0.2)\n",
"\n",
"# Initial trajectory : can be obtained with shooting from the point (0, 0) in +x and -x directions\n",
"# have to obtain it\n",
"\n",
"??paths.engines.toy.integrators.LeapfrogVerletIntegrator\n",
"??paths.engines.openmmp"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": []
}
],
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"name": "python2"
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"file_extension": ".py",
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"name": "python",
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"nbformat": 4,
"nbformat_minor": 1
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