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Test PR for PCVCOMM#38

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Iximiel wants to merge 124 commits intomasterIximiel/plumed2:masterfrom pycvCommIximiel/plumed2:pycvCommCopy head branch name to clipboard

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Commits on Oct 17, 2019

• Attempting merge of pycv in v2.6

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Commits on Oct 18, 2019

• install PYCV prereqs and set PYTHON_BIN to python3

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• workaround the request for documenting components by adding the "py-" prefix to each

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• Delete README.md.upstream

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• plumed-nest entry

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Commits on Oct 21, 2019

• Update README.md

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Commits on May 23, 2020

• Merge tag 'v2.6.0' into v2.6-pycv-devel

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• update pybind to 2.5.0

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• readme

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• readme

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• add versions

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• add versions

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Commits on Sep 5, 2022

• Merge tag 'v2.8.0' into v2.8-pycv-devel

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• regtest fixed

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• Attempting merge of pycv in v2.6

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• install PYCV prereqs and set PYTHON_BIN to python3

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• workaround the request for documenting components by adding the "py-" prefix to each

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• Delete README.md.upstream

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• plumed-nest entry

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• Update README.md

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• update pybind to 2.5.0

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• add versions

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• add versions

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• regtest fixed

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• update pybind 2.10.0

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• travis restore

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Commits on May 15, 2023

• add --embed for python

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Commits on May 16, 2023

• Merge remote-tracking branch 'origin/v2.8-pycv-devel' into pycvComm

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• remove possibly unused options for conda builds

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Commits on Jun 9, 2023

• modernized the python interface

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• updated gitignores

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• added a test for the scopedIntepreter

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Commits on Jun 13, 2023

• adjusted the tests

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Commits on Jun 14, 2023

• Merge branch 'v2.8-pycv-devel' of https://github.com/giorginolab/plumed2-pycv into pycvComm

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Commits on Jun 19, 2023

• the base functionality is there

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• now without verbose overloads

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Commits on Jun 20, 2023

• setting up a better interface

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• passes the tests :)

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• small cosmetic changes

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• adding some "unit tests" to pyVector3d

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Commits on Jun 21, 2023

• added and tested the interface to getPositions

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• consolidating tests

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• added a toNumpy method for vector3D

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Commits on Jun 28, 2023

• the example should figure more clear now

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Commits on Aug 1, 2023

• added a test for the pbcs

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Commits on Sep 21, 2023

• now you can get the atomic positions as a np array

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Commits on Sep 22, 2023

• moved the embedded module in a separate source

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• added an interface to the Pbcs

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Commits on Sep 25, 2023

• moved test for clarity

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• adding getBox and getInvBox

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Commits on Sep 27, 2023

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• run astyle

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Commits on Oct 2, 2023

• Changed the multicomponent return format

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• added the skeleton for the update func

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Commits on Oct 3, 2023

• added a way to make data persist

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Commits on Oct 12, 2023

• added charge and mass accessors but no tests

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• added charge and mass accessors but no tests

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• Merge branch 'pycvCommUpdate' of https://github.com/Iximiel/plumed2 into pycvCommUpdate

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Commits on Oct 16, 2023

• first draft for the NL

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Commits on Oct 17, 2023

• NL works, adding a test-example for the coordination

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• the COORDINATIOn works (but no virial and devs)

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• added virial (for single value)

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• astyle'd

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• setup rt-coord to test the virial

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• now the comment is more truthful

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Commits on Nov 9, 2023

• merged and changed how to compile the so

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• unification of the return interface

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• udpated tests + added list or tuple compatibility for return

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• added getAbsoluteIndex

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Commits on Nov 10, 2023

• change in how AbsoluteIndexes are got

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• preparing to add array getter for mass and charges

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• Merge branch 'pycvCommUpdate' into pycvColvarMethods

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• added masses an charges array

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• f Added some infomration on the ongoing MD

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• set up the tests to be easier to work with

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Commits on Nov 14, 2023

• set up the test for makeWhole

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• some reordering in the code

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• moved the tree of pycv

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• removed pybind11 from the directory

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• moved the tree of pycv

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• set up a rationale for installation/compilation

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• moved also the tests

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• clearer readme

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Commits on Nov 16, 2023

• Merge remote-tracking branch 'home/master' into pycvTree

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• updated the LOAD to use the GLOBAL kw

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• preparing init for returning dictionary

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Commits on Nov 23, 2023

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• added a "doc" example

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• setting up function

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• preparinf for the emebedding

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Commits on Nov 24, 2023

• tested mdInfo in function

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• now the function is embedded

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• changed how to threat errors, types and some movements

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• added a test for func derivatives

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• added arguments returned as ndarray

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• added components to pcvFunc

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• applyed astyle

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• applyed astyle

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• added some methods for function arguments

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Commits on Nov 29, 2023

• moved pycv in a 'plugins' folder

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• Removing modifications to the respect of the master branch

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• rmoved the old pycv tests

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• merging the readmes

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• Updated the readme

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• expanding the manual

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• expanding the manual : function calls

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Commits on Nov 30, 2023

• expanding the readme

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• SimplerAbsolute Indexes, squashed commit of the following:

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• added "make check" also in the plugin dir

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• trying to improve the readability of the pyModule

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• removed a few warning, changed some license headers

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• tested len(NL) and changed how size is returned

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• finished the "minidocumentation" in the readme

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• moved the interface documentation

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• corrected some some typeo

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• corrected some change agains master

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• cleaning the pycv dir

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Commits on Dec 1, 2023

• removed hidden visibility warning in compilation

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• Removed the warnings with the currently active flags

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Commits on Dec 4, 2023

• removed jax test

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Commits on Dec 6, 2023

• Added PyCV to the standard plumed CI

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• reverted an error in the CI

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• removed aspace change in the linux WF

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