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Wolf final#28

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GregorySchwing wants to merge 237 commits intoaddRCUTGregorySchwing/GOMC:addRCUTfrom wolf_finalGregorySchwing/GOMC:wolf_finalCopy head branch name to clipboard

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Commits

Commits on Sep 22, 2021

• first push

  

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  a60fc40

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• merged wolf and targetswap changes to config setup

  

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  dda48c9

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• fix SwapCorrection continue term by adding an abs, also differentiate Vlugt and Cassandra. ConfigSetup was treating them the same.

  

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• add metamake and config setup

  

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Commits on Oct 12, 2021

• pass wolf boolean to GPU kernels

  

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• Push

  

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Commits on Oct 13, 2021

• Energy and FFParticle on GPU done.

  

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• Pass to all the diff functions in En

  

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• fix tab. Need to make sure InRCut checks the RCutCoul on GPU, also explore whether RCut or RCutCoul should be used for Shift Coul

  

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• Modified kernels to return value. We already were passing rCutCoul box.

  

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• make vertical the method sigs and moving to consistent and clear var names.

  

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• En builds

  

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• EN builds

  

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Commits on Oct 14, 2021

• Pass parameters to CalcCoulForce

  

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• PArticle

  

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• Shift

  

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• Middle methods

  

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• All potentials now support wolf for force and energy on the GPU

  

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• Removed openMP from Wolf CPU

  

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Commits on Oct 15, 2021

• Add alot of err chk

  

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  16b63ab

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• found the bug

  

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Commits on Oct 18, 2021

• fix the potentials in GPU

  

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  bdd1f97

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Commits on Oct 21, 2021

• Fixed WolfFactor2

  

  GregorySchwing

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  b4f97d8

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• Self term was 2 times to large.

  

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  0b27ecf

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Commits on Oct 22, 2021

• Add Cassandra's QQfact. Left old one in comment

  

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Commits on Oct 23, 2021

• increased precision.

  

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  3c33bef

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Commits on Oct 26, 2021

• Changed variable we add DSF term in Correction methods. Initial energy calculation is now 0.06% different from Cassandra.

  

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Commits on Oct 28, 2021

• If wolf is true and electrostatic false, set electrostatic true

  

  GregorySchwing

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  45f13dc

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Commits on Nov 2, 2021

• first push

  

  GregorySchwing

  committed
  0bafeec

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• merged wolf and targetswap changes to config setup

  

  GregorySchwing

  committed
  e17b89f

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• fix SwapCorrection continue term by adding an abs, also differentiate Vlugt and Cassandra. ConfigSetup was treating them the same.

  

  GregorySchwing

  committed
  ec4c4b5

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• add metamake and config setup

  

  GregorySchwing

  committed
  fc9dda9

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• pass wolf boolean to GPU kernels

  

  GregorySchwing

  committed
  2ea2153

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• Push

  

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  f578cfd

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• Energy and FFParticle on GPU done.

  

  GregorySchwing

  committed
  efe8317

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• Pass to all the diff functions in En

  

  GregorySchwing

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  72400ca

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• fix tab. Need to make sure InRCut checks the RCutCoul on GPU, also explore whether RCut or RCutCoul should be used for Shift Coul

  

  GregorySchwing

  committed
  a0ce586

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• Modified kernels to return value. We already were passing rCutCoul box.

  

  GregorySchwing

  committed
  3c2702e

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• make vertical the method sigs and moving to consistent and clear var names.

  

  GregorySchwing

  committed
  1b98256

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• En builds

  

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  1fb88ad

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• EN builds

  

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  8a987f9

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• Pass parameters to CalcCoulForce

  

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  32cf5b2

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• PArticle

  

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  bd7723a

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• Shift

  

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  2c0f580

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• Middle methods

  

  GregorySchwing

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  ad7842d

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• All potentials now support wolf for force and energy on the GPU

  

  GregorySchwing

  committed
  cab118e

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• Removed openMP from Wolf CPU

  

  GregorySchwing

  committed
  57b9a6b

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• Add alot of err chk

  

  GregorySchwing

  committed
  0569135

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• found the bug

  

  GregorySchwing

  committed
  e5a0036

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• fix the potentials in GPU

  

  GregorySchwing

  committed
  b2ba569

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• Fixed WolfFactor2

  

  GregorySchwing

  committed
  f49abd9

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• Self term was 2 times to large.

  

  GregorySchwing

  committed
  cba27fe

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• Add Cassandra's QQfact. Left old one in comment

  

  GregorySchwing

  committed
  5d4e68f

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• increased precision.

  

  GregorySchwing

  committed
  d34c84a

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• Changed variable we add DSF term in Correction methods. Initial energy calculation is now 0.06% different from Cassandra.

  

  GregorySchwing

  committed
  43c558a

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• If wolf is true and electrostatic false, set electrostatic true

  

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  committed
  d089262

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• Rebased wolfFromDev with development

  

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Commits on Nov 8, 2021

• Merge error in metamake.sh

  

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• More merge errors

  

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Commits on Nov 30, 2021

• added option to exclude 1-N

  

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Commits on Feb 2, 2022

• Added config files to calibrate wolf

  

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Commits on Feb 6, 2022

• Add wolfoutput files

  

  GregorySchwing

  committed
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• working on initting the wolfcal

  

  GregorySchwing

  committed
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• Added WolfCalibrationFreq to output options in config file

  

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• Use ranges to set number of calib points

  

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Commits on Feb 7, 2022

• Realizing I need to call the SystemTotal method in CalcEn with differing values of Rcut and alpha. I will have to write a method which takes an array of rcuts and alphas and an array of energy valu…

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Commits on Feb 13, 2022

• started modifying FFParticle methods.

  

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• Revert "started modifying FFParticle methods."

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• Revert "Revert "started modifying FFParticle methods.""

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• Revert "Revert "Revert "started modifying FFParticle methods."""

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• using default indexes to determine whether I am calibrating or running a production sim

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  committed
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• pass a wolf calibration flag.

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Commits on Feb 14, 2022

• Revert "pass a wolf calibration flag."

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• set numberofRcuts to 1

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  dda28b7

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• renamed var and added var to CalcCoulVir

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  committed
  2039e22

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• decided on a pattern

  GregorySchwing

  committed
  9c6888f

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• moved the processing of the config file to Forcefield Cobj initialization

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  committed
  0b5e59d

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• pass stat val wolfcal object to ff

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  committed
  ec67e9e

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• updated most of ff classes to use double pointers and default arguments

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  committed
  bacbee3

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• need to update wolfAlpha now

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  committed
  19cad05

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• need to update wolfFactor terms. not sure how I will do this yet

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Commits on Feb 16, 2022

• use correct data structures for all but Wolf class

  GregorySchwing

  committed
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• temporary made wolf class only use config file alpha and rcut

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  committed
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• dynamically allocate double and triple pointers. in Forcefield

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  committed
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• alloc and dealloc mem methods written

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  7b0244a

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• Think I'm initting the calibration vals correctly

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  19aae34

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Commits on Feb 17, 2022

• overwrite last val if explicitlyAddEnd true

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  committed
  32aa504

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• can test wolf cal output header

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• actually call writeheader

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  committed
  8a45022

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• wolf cal works

  

  GregorySchwing

  committed
  13802a8

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• should calculate energies for all alphas and rcuts

  

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  committed
  a6ee4ad

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• WRite par files for grace. I likely will write separate files separated by rcut for grace viz. The whole csv will be used for solving the optimum alpha rcut for the next iteration

  

  GregorySchwing

  committed
  3954196

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• switch from wolf to ewald for ref pairs. Also init the ewald refewald object

  

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  committed
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• actually use the indices I pass...

  

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  committed
  ca7dfa9

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• dont turn on ewald yet..

  

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Commits on Feb 18, 2022

• add a comment

  

  GregorySchwing

  committed
  6289eaf

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Commits on Feb 19, 2022

• updated wolf class for calibrating

  

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  3f264df

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• self and intra. now need virial

  

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Commits on Feb 20, 2022

• separate Energy term intra into vdw and real

  

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  8758185

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• dont pass alpha to calc1-4Coul

  

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  committed
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• builds. Going to do this the clean way. I just need a way to pass indexrcut to molintra

  

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  committed
  3a95767

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• intra done

  

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  81b5a22

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Commits on Feb 21, 2022

• Wrote one method to do the full energy calc. Still need to test, and figure out a way to get the reference value

  

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  committed
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• new approach produces reasonable xmgrace energy plots

  

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  d7700ed

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• seems to be working

  

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• done

  

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Commits on Feb 27, 2022

• removed the duplicate columns in wolf cal file.

  

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• machinery to swap coul kinds and wolf kinds in cal

  

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  committed
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• wrote methods to get and set coul and wolf kind. need to expand the energy trip pointer to 5 pointers

  

  GregorySchwing

  committed
  7922553

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• wrapped up method cal. Might be biased to use one method to evolve system

  

  GregorySchwing

  committed
  4cc2fe4

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• fix bug in for loop for coul kinds

  

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  committed
  235748d

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• dont calc cal energy for 0,0 rcut,alpha

  

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Commits on Mar 1, 2022

• fixed wolfCalOut

  

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  committed
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• fix par file

  

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• finalize

  

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  2aec7ed

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Commits on Apr 5, 2022

• renamed cassandra to vlugt with intra cutoff

  

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Commits on Apr 12, 2022

• use coulkind...

  

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  committed
  43fd2e7

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• fix initialization of wolf and ewald in calibration

  

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  committed
  4dba335

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• had to make get and set wolf and coul kind methods virtual

  

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Commits on Apr 15, 2022

• print memory in console

  

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  committed
  490867a

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• wolfCal was defaulting to enabled

  

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  committed
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• Activate wolf cal enable in datastructure

  

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Commits on Apr 18, 2022

• hopefully works on intel

  

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  committed
  41ec9f1

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• realizing I have a bug in intra nonbonded wolf

  

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  committed
  61b576f

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• make sure rcutSeq uses the largest rcutcoul calib

  

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  committed
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• think I have a working Vlugt

  

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  committed
  d4eabce

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• removed dsf potential from intra correction

  

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  committed
  6e8c60e

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• remove more intra dsf stuff that shouldnt be there

  

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  committed
  a9d6b71

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• fix self

  

  GregorySchwing

  committed
  6cd6b3f

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• use unified intra iteration

  

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• Revert "use unified intra iteration"

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• change behavior of inter. fix self

  

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  committed
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• last thing to check is wolf kind when calculating reference.

  

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  committed
  8aa7259

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• fix switch between ewald and wolf

  

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  committed
  1e0b596

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• removed unused vars in CalcEn, ewald and wolf. only electrostatic bool is needed

  

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Commits on Apr 19, 2022

• add some couts

  

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  committed
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• use std::abs

  

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  committed
  f78e98d

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• cal done

  

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  committed
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• cassandra is spot on for correction and self. Cassandra uses dsf potential for intra electrostatic. vlugt doesnt

  

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  committed
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Commits on Apr 20, 2022

• bug fix

  

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  committed
  9e1f5cc

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Commits on Apr 26, 2022

• GPU version builds. doesnt support calibrate, and still need to test

  

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Commits on Apr 27, 2022

• Revert "GPU version builds. doesnt support calibrate, and still need to test"

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• started toward flat

  

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• all ff cutoffs

  

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  4d4aac6

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• fix alphas.

  

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  committed
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• rCutCoul.

  

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  4ddb354

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• should set the startIndex of each wolf ffactor array

  

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  6a8d97c

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• should set the startIndex of each wolf ffactor array

  

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• closer

  

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• might have to sell

  

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• directly pass wolfalpha nad rcc

  

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• directly pass method sig

  

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• keep going

  

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  45136e0

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• CalcCoul and CalCoulVir done

  

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• CalcCoul and CalCoulVir done

  

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• CalcCoul and CalCoulVir done

  

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• CalcCoul and CalCoulVir done

  

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• CalcCoul and CalCoulVir done

  

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• CalcCoul and CalCoulVir done

  

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• CalcCoul and CalCoulVir done

  

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• CalcCoul and CalCoulVir done

  

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• done

  

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• done

  

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• done

  

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• Standard wolf should work

  

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Commits on Apr 28, 2022

• revert GPU and move cal into new file

  

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• :w:

  

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• BIITFO

  

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• real wrong

  

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• need to debug

  

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• index function seems to work and removed explicitly add logic

  

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• working prototype

  

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Commits on Apr 29, 2022

• directly leaking memory since ff is type wolf

  

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  11289df

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• starting to work

  

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• starting to work

  

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• back to reference. still leaking 64 bytes

  

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  7eb8e19

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Commits on May 2, 2022

• add nemetmc example

  

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  a0a2094

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• Revert "add nemetmc example"

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  8eb5774

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• use new box inter method for vol t

  

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  b987b05

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• fix intra

  

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  83d54c7

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• should be done cal

  

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Commits on May 16, 2022

• remove endian test header

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• remove lib endian

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• add endian back

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  90f18d7

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• add this till I get endian removed

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  9c2416b

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• crankshaft was calling ewald. I really should separate the ewald and wolf classes.

  

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• add header for swapcorr wolf

  

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• add memory usage right after cpu alloc

  

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  84de2a9

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• move before cuda

  

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Commits on Jun 1, 2022

• fix cub

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  1bfd6a8

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Commits on Jul 15, 2022

• moved wolf potential to its own line in config file

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Commits on Jul 18, 2022

• wolf cal isnt correctly calculating the ewald ref

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• ref ewald matcxhes except for lrc and lj???

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  45ab8e9

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• should work now

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  06b4c70

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Commits on Aug 3, 2022

• use one SwapCorr method. There was some semantic difference where lambda was assumed to 1 and thus it wasnt multiplied. This was causing problems for my Wolf implementation. Also, fixed SwapCorr fo…

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Commits on Sep 5, 2022

• prevent double free

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  982c097

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• fix changeself wolf

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Commits on Sep 25, 2022

• compile error in molex1

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  431aea1

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Commits on Sep 26, 2022

• only require 1 set rcut alpha for gcmc

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• also use NB for wolf cal methods

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• BOXES_WITH_U_NB in WolfCalOutput

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• calibrate virial correctly and also, use gpu for boxinter wolf cal

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• add to prago mp

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• should be able to calibrate on the gpu

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• err in obj building

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Commits on Sep 27, 2022

• gpu and cpu match for wolf cal.

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  7519aaf

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• make sure ref sim uses the orig rcut coul. gpu and cpu diff by 0.00005%

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  36c54f9

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Commits on Sep 28, 2022

• cal now uses ewald

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Commits on Sep 29, 2022

• free wolf vars

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  c7c4ef0

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Commits on Oct 11, 2022

• only use TotalElec for calibrating wolf

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  d73bc37

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Commits on Oct 12, 2022

• finished commenting out the override rcut for vlugt. should make calibration equal reality

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  e5da9d4

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• dont calibrate hybrd

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  e601d2f

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• dont calibrate hybrd

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  0071df1

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Commits on Oct 13, 2022

• Revert "finished commenting out the override rcut for vlugt. should make calibration equal reality"

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Commits on Oct 16, 2022

• fix clock

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Commits on Nov 5, 2022

• fix gemc_nvt

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  eea8780

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• fix swap self method

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  21de13a

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Commits on Nov 6, 2022

• pass arch

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  b58bada

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Commits on Nov 9, 2022

• fixed correction term. Vlugt/Cassandra was correct. Gross was incorrect

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  fdf08f1

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Commits on Nov 10, 2022

• pass entire rcc ptr :(

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  fb8d90b

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• same fix for force

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Commits on Nov 11, 2022

• fix get index method

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  71d9485

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• final bug fix for calibrating gemc

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  c762eb0

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• fix correction term

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  8c1e73a

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• Fix maxs bug locally

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• builds

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  3651ff8

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• F

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  14dced0

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Commits on Nov 14, 2022

• fixed self temr

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  e6329c0

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• ast fix..

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  8899940

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• fix correction term, but shouldnt explain error..

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  57c7cf2

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Commits on Nov 18, 2022

• fixed swap corr. still need to pass dest or source box though..

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  54ffb21

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• fixed gemc wolf

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Commits on Nov 26, 2022

• dont add wf1 to hybrid without scaling

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• changed hybrid wolf to be the fixed waibel2018 implementation

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• cast to int in method sig

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• update headers

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Commits on Nov 27, 2022

• iniitialize wolfCal boolean in ff

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