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Merged
dwhswenson merged 11 commits into from
Oct 6, 2018
Merged

Updates to Examples #798

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df913bd
Attempt to fix for old openmmtools as well as new
dwhswenson Apr 16, 2018
78382fc
add import openmmtools.integrators
dwhswenson Apr 16, 2018
9f0fbad
Updates to examples in advance of paper versions
dwhswenson May 5, 2018
bae03cc
update total decorrelated trajectories (fixed TPS)
dwhswenson May 9, 2018
fb91bb9
Merge remote-tracking branch 'upstream/master' into examples
dwhswenson Jun 4, 2018
e931343
Merge branch 'fix_openmmtools_rename' into examples
dwhswenson Jun 4, 2018
029f21c
update examples
dwhswenson Jun 4, 2018
7cea501
Merge remote-tracking branch 'upstream/master' into examples
dwhswenson Sep 13, 2018
35c8a3d
Update examples to match manuscript text
dwhswenson Sep 19, 2018
1872e68
update toy_mistis example to match paper text
dwhswenson Sep 27, 2018
986a683
Merge remote-tracking branch 'upstream/master' into examples
dwhswenson Sep 27, 2018
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Update examples to match manuscript text
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@dwhswenson
dwhswenson committed Sep 19, 2018
commit 35c8a3d52178abf0d58a5becddf044faf6401a8a
23 changes: 12 additions & 11 deletions examples/alanine_dipeptide_tps/AD_tps_1_trajectory.ipynb
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Expand Up @@ -31,7 +31,7 @@
"import matplotlib.pyplot as plt\n",
"import openpathsampling as paths\n",
"\n",
"import openpathsampling.engines.openmm as peng_omm\n",
"import openpathsampling.engines.openmm as omm\n",
"from simtk.openmm import app\n",
"import simtk.openmm as mm\n",
"import simtk.unit as unit\n",
Expand Down Expand Up @@ -97,11 +97,11 @@
},
"outputs": [],
"source": [
"template = peng_omm.snapshot_from_pdb(\"../resources/AD_initial_frame.pdb\")\n",
"template = omm.snapshot_from_pdb(\"../resources/AD_initial_frame.pdb\")\n",
"openmm_properties = {'OpenCLPrecision': 'mixed'}\n",
"engine_options = {\n",
" 'n_frames_max': 2000,\n",
" 'nsteps_per_frame': 10\n",
" 'n_steps_per_frame': 10,\n",
" 'n_frames_max': 2000\n",
"}"
]
},
Expand All @@ -111,7 +111,7 @@
"metadata": {},
"outputs": [],
"source": [
"hi_T_engine = peng_omm.Engine(\n",
"hi_T_engine = omm.Engine(\n",
" template.topology, \n",
" system, \n",
" hi_T_integrator, \n",
Expand Down Expand Up @@ -159,11 +159,12 @@
"source": [
"# define the states\n",
"deg = 180.0/np.pi\n",
"C_7eq = (paths.PeriodicCVDefinedVolume(phi, lambda_min=-180/deg, lambda_max=0/deg, \n",
" period_min=-np.pi, period_max=np.pi) &\n",
" paths.PeriodicCVDefinedVolume(psi, lambda_min=100/deg, lambda_max=200/deg,\n",
" period_min=-np.pi, period_max=np.pi)\n",
" ).named(\"C_7eq\")\n",
"C_7eq = (\n",
" paths.PeriodicCVDefinedVolume(phi, lambda_min=-180/deg, lambda_max=0/deg, \n",
" period_min=-np.pi, period_max=np.pi) &\n",
" paths.PeriodicCVDefinedVolume(psi, lambda_min=100/deg, lambda_max=200/deg,\n",
" period_min=-np.pi, period_max=np.pi)\n",
").named(\"C_7eq\")\n",
"# similarly, without bothering with the labels:\n",
"alpha_R = (paths.PeriodicCVDefinedVolume(phi, -180/deg, 0/deg, -np.pi, np.pi) &\n",
" paths.PeriodicCVDefinedVolume(psi, -100/deg, 0/deg, -np.pi, np.pi)).named(\"alpha_R\")"
Expand Down Expand Up @@ -300,7 +301,7 @@
" 2.0*unit.femtoseconds\n",
")\n",
"integrator.setConstraintTolerance(0.00001)\n",
"engine = peng_omm.Engine(\n",
"engine = omm.Engine(\n",
" template.topology, \n",
" system, \n",
" integrator, \n",
Expand Down
7 changes: 3 additions & 4 deletions examples/alanine_dipeptide_tps/AD_tps_3a_analysis_flex.ipynb
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Expand Up @@ -356,11 +356,10 @@
}
],
"source": [
"replica_history = ops_vis.ReplicaEvolution(replica=0)\n",
"tree = ops_vis.PathTree(\n",
" flexible.steps[0:25],\n",
" ops_vis.ReplicaEvolution(\n",
" replica=0\n",
" )\n",
" replica_history\n",
")\n",
"tree.options.css['scale_x'] = 3\n",
"\n",
Expand Down Expand Up @@ -888,7 +887,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython2",
"version": "2.7.13"
"version": "2.7.15"
}
},
"nbformat": 4,
Expand Down