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JNapoli wants to merge 144 commits intoleeping:masterleeping/forcebalance:masterfrom JNapoli:masterJNapoli/forcebalance:masterCopy head branch name to clipboard

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Commits

Commits on Jan 23, 2014

• Fix to polarization correction

  

  Frank Lin

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Commits on Jan 28, 2014

• Merge branch 'master' of github.com:leeping/forcebalance

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  Frank Lin

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Commits on Feb 11, 2014

• Merge branch 'master' of https://github.com/leeping/forcebalance

  

  Frank Lin

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• Begin adding interface for RP contraction

  

  Frank Lin

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Commits on Mar 19, 2014

• Added RPMD kinetic energy calculation

  

  Frank Lin

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• Merge branch 'master' of github.com:leeping/forcebalance

  

  Frank Lin

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• test commit

  

  Frank Lin

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• Test

  

  Frank Lin

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• TEST

  

  Frank Lin

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• test1

  

  Frank Lin

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Commits on Mar 20, 2014

• CustomBondForce

  

  Frank Lin

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• CustomBondForce(error in getPerBondParameterName)

  

  Frank Lin

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Commits on Mar 22, 2014

• CustomBondForce(working version)

  

  Frank Lin

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Commits on Mar 23, 2014

• RPMD input should be list of integer not number

  

  Frank Lin

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Commits on Mar 26, 2014

• Energy estimator

  

  Frank Lin

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• Merge branch 'master' of github.com:leeping/forcebalance

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  Frank Lin

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• Merge branch 'master' of github.com:leeping/forcebalance

  

  Frank Lin

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• Update rpmd energy estimating(centroid instead of primitive energy estimator)

  

  Frank Lin

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Commits on Mar 27, 2014

• Centroid Energy Estimator

  

  Frank Lin

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Commits on Apr 2, 2014

• test setposition

  

  Frank Lin

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Commits on Apr 4, 2014

• RPMD set_position (test)

  

  Frank Lin

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Commits on Apr 5, 2014

• Undo get multipole function

  

  Frank Lin

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Commits on Apr 7, 2014

• update energy estimator

  

  Frank Lin

  committed
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Commits on Apr 9, 2014

• Implement Potential and Kinetic energy calculators for RPMD simulation as function

  

  Frank Lin

  committed
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• Replace code that calculate quantum kinetic energy by function

  

  Frank Lin

  committed
  83817f3

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• Fix a few RPMD related bug

  

  Frank Lin

  committed
  fc50a07

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• Adding centroid position calculator

  

  Frank Lin

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• Change nothing, just test

  

  Frank Lin

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  9cdf137

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• Fix some minor(but important!) bug.

  

  Frank Lin

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• Try again.

  

  Frank Lin

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Commits on Apr 10, 2014

• RPMD Virtual Site

  

  Frank Lin

  committed
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• change nothing

  

  Frank Lin

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  96bea44

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• fix syntax error

  

  Frank Lin

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• Use centroid KE to calculate KE in RPMD

  

  Frank Lin

  committed
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Commits on May 5, 2014

• Edit the fractionation ratio energy function

  

  Frank Lin

  committed
  cc9abba

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• edit HD

  

  Frank Lin

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• ":"

  

  Frank Lin

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• undo last step

  

  Frank Lin

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Commits on May 6, 2014

• undo

  

  Frank Lin

  committed
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Commits on May 14, 2014

• Merge branch 'master' of https://github.com/frankmenglin/forcebalance

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  JNapoli

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Commits on May 16, 2014

• Fix some verbose inline comments. Mainly testing commit/push. No substantial change.

  JNapoli

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• Change rpmd_beads to rpmd_opts for clarity.

  JNapoli

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Commits on May 18, 2014

• Add support for storing and setting positions for RPMD simulation.

  JNapoli

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• Revise code for setting virtual sites in RPMD images.

  JNapoli

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Commits on May 19, 2014

• Incorporate modifications suggested by Lee-Ping. Remove redundancies.

  JNapoli

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• Begin adding RPMD test files.

  JNapoli

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Commits on May 28, 2014

• Updated cctools version

  

  Joseph Napoli

  committed
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• Merge branch 'master' of github.com:leeping/forcebalance

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  Joseph Napoli

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Commits on Jun 2, 2014

• Merge branch 'master' of github.com:leeping/forcebalance

  

  Joseph Napoli

  committed
  086cdb3

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• Fixed some stuff.

  JNapoli

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• Merge branch 'master' of github.com:JNapoli/forcebalance

  JNapoli

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Commits on Jun 3, 2014

• Add code to average dipole values over all copies of an RPMD system.

  JNapoli

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Commits on Jun 4, 2014

• Commit cctools changes.

  

  Joseph Napoli

  committed
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• Fix merge conflict.

  

  Joseph Napoli

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Commits on Jun 9, 2014

• Enable use of PDB file for coordinates.

  JNapoli

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• Merge branch 'master' of github.com:JNapoli/forcebalance

  JNapoli

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Commits on Jun 22, 2014

• Begin validation script for RPMD functionality. Modify openmmio.py to turn off rigidWater constraints in case of RPMD.

  JNapoli

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• Remove unnecessary code in test script. Add directory containing qtip4pf xml and pdb files.

  JNapoli

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Commits on Jun 25, 2014

• Begin fix for constraint modification code.

  JNapoli

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  672e454

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• Typo fix

  JNapoli

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  945bc15

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• Fix method call syntax. Whoops.

  JNapoli

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  7e59ed2

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• Clean up update_simulation() and constraint checking.

  JNapoli

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• Remove stray print statement.

  JNapoli

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Commits on Jun 26, 2014

• Revise RPMD unit test.

  

  Joe Napoli

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• Revise xyz_rpmd data structure; add RPMD functionality to evaluate_(); add function to get forces.

  JNapoli

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  4ed220c

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• Undo get_dipole() modification and put that functionality in evaluate_one_().

  JNapoli

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  6fe3b13

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• Fix get_forces() bug.

  JNapoli

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  6815c71

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• We had been assuming non-empty parameter vectors; fixed now?

  JNapoli

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• Merge branch 'master' of github.com:leeping/forcebalance

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  JNapoli

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• Shorten test case

  JNapoli

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• Fixes for unit test

  JNapoli

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  efa1c88

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• Updated OpenMM on Jenkins

  JNapoli

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Commits on Jun 27, 2014

• Remove verbosity option in unit test.

  JNapoli

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• Clean and delete unnecessary lines.

  JNapoli

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  a8e8b00

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• Fix setting of virtural sites and postprocessing of dipoles.

  JNapoli

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Commits on Jun 28, 2014

• Add dipole test to test_rpmd.py

  JNapoli

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• Fix indentation issue in rpmd_dips().

  JNapoli

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Commits on Jul 7, 2014

• Test new centroid virial estimator.

  JNapoli

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Commits on Jul 8, 2014

• Try setting positions a different way.

  

  Joe Napoli

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Commits on Jul 10, 2014

• Add functions to test first terms in energy estimators.

  JNapoli

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• Another test.

  JNapoli

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Commits on Jul 31, 2014

• Add functions to calculate Cv for NVT simulation.

  JNapoli

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Commits on Sep 18, 2014

• Merge branch 'master' of github.com:leeping/forcebalance

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  JNapoli

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• Update energy estimators to latest version. Clean up functions that were incorrect.

  JNapoli

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• Commit most recent changes for pull to ICME.

  JNapoli

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Commits on Oct 13, 2014

• Incorporate calculation of Cp analytic derivative for RPMD.

  JNapoli

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Commits on Oct 14, 2014

• Revert to original version of rpmd unit test

  JNapoli

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Commits on Oct 23, 2014

• Push changes for pull on ICME

  JNapoli

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Commits on Oct 24, 2014

• Merge branch 'master' of https://github.com/chenchens/forcebalance

  JNapoli

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• Merge branch 'master' of https://github.com/chenchens/forcebalance

  

  joe

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Commits on Oct 30, 2014

• Merge leeping master

  

  joe

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Commits on Nov 2, 2014

• Clean up old changes

  

  joe

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• Merge branch 'master' of github.com:JNapoli/forcebalance

  JNapoli

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Commits on Nov 5, 2014

• Add CopyCustomBondedParameters to use with qtip4pf

  JNapoli

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Commits on Nov 8, 2014

• Oops

  JNapoli

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Commits on Nov 12, 2014

• Add code for centroid virial gradient.

  JNapoli

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• Revise rpmd gradient method.

  JNapoli

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Commits on Nov 16, 2014

• Revise postprocessing and gradient calculations for RPMD

  JNapoli

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Commits on Jan 19, 2015

• Push for pull to ICME

  JNapoli

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Commits on Jan 24, 2015

• Fix thermal expansion

  JNapoli

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• Fix variable name error

  JNapoli

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Commits on Jan 26, 2015

• Standardize control flow. Fix RPMDH bug.

  JNapoli

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Commits on Feb 3, 2015

• Standardize control flow for PIMD.

  JNapoli

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Commits on Feb 11, 2015

• Incorporate RPMD specific gradients into liquid.py

  JNapoli

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Commits on Feb 12, 2015

• Add RPMD gradients to liquid.py

  JNapoli

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  b0a2930

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• Finish incorporating derivatives into liquid.py

  JNapoli

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  a41b978

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• Minor change to read() method.

  JNapoli

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  202744b

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• Make npt_result pickle more general

  JNapoli

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Commits on Feb 13, 2015

• Fix variable swap in npt_result pickle

  JNapoli

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Commits on Feb 16, 2015

• Change the way the heat capacity correction is calculated. Reflect this change in npt.py and liquid.py.

  JNapoli

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Commits on Feb 21, 2015

• Add code for fitting total energy w/ centroid virial QKE. This tests the CVQKE gradient.

  JNapoli

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• Make sure parser doesn't break.

  JNapoli

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Commits on Feb 24, 2015

• Whoops

  JNapoli

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• Fix reference before assignment

  JNapoli

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Commits on Feb 28, 2015

• Remove centroid virial quantum kinetic energy liquid target. Enable centroid virial and primitive quantum kinetic energy targets.

  JNapoli

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• Use RPMDMonteCarloBarostat for PIMD simulations.

  JNapoli

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• Fix division error and setting of n_mcbarostat.

  JNapoli

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Commits on Mar 14, 2015

• Replace H in alpha grad with RPMDH

  JNapoli

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Commits on Mar 25, 2015

• CUDA platform is much faster for PIMD gas phase simulation

  JNapoli

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Commits on Apr 16, 2015

• Change nonbonded parameters

  JNapoli

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• Ensure that defaults make it in

  JNapoli

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Commits on Apr 17, 2015

• Add pbc condition to setting of nonbonded cutoffs

  JNapoli

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Commits on May 1, 2015

• Add code to save centroids and only store one system copy.

  JNapoli

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Commits on Jul 7, 2015

• Fix a reference before assignment and nonbonded method in preparation for iAMOEBA

  JNapoli

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Commits on Aug 26, 2015

• Write AbInitio_LAMMPS target

  JNapoli

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Commits on Aug 27, 2015

• Some small bug fixes

  JNapoli

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Commits on Oct 19, 2015

• Lammps branch is up to date

  JNapoli

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  96e7cfe

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• Add logic for only using one bead in postprocessing

  JNapoli

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• Device number change for testing

  JNapoli

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Commits on Oct 27, 2015

• get_V function now returns forces if requested

  JNapoli

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Commits on Nov 9, 2015

• Merge branch 'lammps'

  JNapoli

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Commits on Nov 16, 2015

• Use reference for gas phase simulation on xstream for now

  

  Joe Anthony Napoli III

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• Debug statement for CUDA device

  

  Joe Anthony Napoli III

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Commits on Nov 17, 2015

• Remove duplicate calculation of centroids. Other minor edits

  

  Joe Anthony Napoli III

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  f8e6a0b

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• Merge branch 'master' of github.com:JNapoli/forcebalance

  JNapoli

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Commits on Nov 21, 2015

• Redo PIMD estimators and write custom reporter for PIMD.

  JNapoli

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• Merge branch 'master' of github.com:JNapoli/forcebalance

  JNapoli

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Commits on Nov 26, 2015

• Delete simulation objects explicitly. Otherwise they crash on Xstream.

  JNapoli

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• Hopefully can use CUDA platform for both simulations now.

  JNapoli

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Commits on Nov 27, 2015

• Fix small bugs

  JNapoli

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  7447ff5

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• Merge branch 'master' of github.com:JNapoli/forcebalance

  JNapoli

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Commits on Dec 2, 2015

• Merge leeping master

  JNapoli

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• Replace molecular_dynamics method with original method. All PIMD code now contained in its own method.

  JNapoli

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Commits on Dec 21, 2015

• Refactor lammpsio calculation of energy series

  JNapoli

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