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Add PME for GIST#889

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drroe merged 101 commits intoAmber-MD:masterfrom
drroe:addGistPme
Apr 4, 2021
Merged

Add PME for GIST#889
drroe merged 101 commits intoAmber-MD:masterfrom
drroe:addGistPme

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@drroe drroe commented Apr 2, 2021

Details in https://doi.org/10.26434/chemrxiv.13140011.v2, soon to be published in JCTC. Updates version to 5.2.0.

This adds particle mesh Ewald to GIST. Right now it is turned off by default, but can be turned on via the new pme keyword. The updated GIST syntax is:

  [help gist]
	[doorder] [doeij] [skipE] [skipS] [refdens <rdval>] [temp <tval>]
	[noimage] [gridcntr <xval> <yval> <zval>] [excludeions]
	[griddim <xval> <yval> <zval>] [gridspacn <spaceval>]
	[prefix <filename prefix>] [ext <grid extension>] [out <output>]
	[info <info>]
	[nopme|pme [cut <cutoff>] [dsumtol <dtol>] [ewcoeff <coeff>]
	 [erfcdx <dx>] [skinnb <skinnb>] [ljswidth <width>]
	 [order <order>] [nfft <nfft1>,<nfft2>,<nfft3>]]

The PME keywords function as they do in the energy command (and indeed, under the hood they are using the same code). The PME code is still a bit of a work in progress in terms of formatting the output, but it is functional as-is.

This PR also improves the automatic shader model detection for the CUDA code, and adds support for CUDA 11. A general overhaul of the CUDA code is overdue...

drroe added 30 commits March 25, 2021 11:11
@drroe
Start adding a new class, GIST_PME, that will inherit from
25ddfe4 
Ewald_ParticleMesh and implement GIST-related PME stuff
@drroe
Add recip and self6 calcs
a4b24c9
@drroe
Add long range correction for gist
767e796
@drroe
Add direct space sum routine.
b225b45
@drroe
Bring HelPME up to PR Amber-MD#54
ca54133
@drroe
Expose sumq and vdw_recip_term via functions
4b50682
@drroe
Add some per-atom vdw stuff needed for PME_GIST
432bf91
@drroe
Expose more of Ewald to inheriting classes
87a6925
@drroe
Expose more of Ewald_ParticleMesh for inherting classes. Add
fe35b81 
implementation of ErfcFxn
@drroe
Add direct space calcs
fc6dcf8
@drroe
Make switch function available to inheriting classes
5b02ce2
@drroe
Fix exclusion array type
edb0972
@drroe
GIST with LJPME not ready for primetime
bc58629
@drroe
Add PmeOptions class.
c6ca56a
@drroe
Add help keywords. Ensure all variables are initialized.
0c6ed64
@drroe
Add functions to return private vars
818fd3f
@drroe
Add Init for Ewald_ParticleMesh with PmeOptions
8c7d477
@drroe
Start adding PME to GIST. Initialize some uninitialized vars
1896bf5
@drroe
Create non-inlined version of adjust for GIST_PME
3973c97
@drroe
Make LJ PME keywords a separate function for things that do not support
0c050e4 
it
@drroe
Start adding PME GIST data sets
35b89ff
@drroe
LJ PME not yet allowed for GIST
4e4740f
@drroe
Ensure energy calc is done for any occupied voxel (occupancy > 0 instead
c5d662c 
of > 1).
@drroe
Update tip4p and tip5p tests for occupancy threshold change
83f9580
@drroe
Finish PME init
a45e21a
@drroe
Add debug level. Do PME init and setup.
4059e93
@drroe
Add solute/water id and solute index arrays
f7f15a4
@drroe
Start adding actual PME calc. Need to save whether atom is solvent or
1cc994c 
solute separate from atom_voxel since we now might care about whether
solute is on or off the grid.
@drroe
atom_voxel_ and atomIsSolute_ arrays will be accessed by atom #
94b6f4e
@drroe
Add PME solute grid assignment
613ce3a
drroe added 12 commits April 1, 2021 10:56
@drroe
Do not run the PME tests for cuda. Slightly increase the test tolerance
7ab7428 
for GPU.
@drroe
Try to fix CUDA compile. Need a better way to determine arch flags...
ea612ea
@drroe
Add list of cuda flags.
d1a36c5
@drroe
Try a better way to set up the shader model flags
35e2503
@drroe
Add shader model cuda version check
c7be209
@drroe
Remove old configure logic
4793d12
@drroe
Consolidate direct space energy calc into one function. Add adjust
86560cd 
energy kernel. Use adjust energy kernel. Make PME GIST output file v3 because of additional PME columns
@drroe
Compare PME GIST output if present. Not uploading it because its too big
f900982 
for GitHub
@drroe
Merge branch 'master' into addGistPme
464d3ec
@drroe
Make GIST PME off the default for now until the output stabilizes.
f6e0018
@drroe
Fix help option
8a346cb
@drroe
Fix GIST and energy command entries
f77ad43
@drroe drroe self-assigned this Apr 2, 2021
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drroe commented Apr 2, 2021 

E: Failed to fetch http://security.ubuntu.com/ubuntu/pool/main/c/curl/libcurl4-gnutls-dev_7.68.0-1ubuntu2.4_amd64.deb  404  Not Found [IP: 52.147.219.192 80]

GRR....it's a bit maddening when the CI framework fails...

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AmberJenkins commented Apr 2, 2021

The PGI build in Jenkins failed.

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lgtm-com bot commented Apr 2, 2021

This pull request introduces 2 alerts when merging f77ad43 into 113407f - view on LGTM.com

new alerts:

  • 2 for FIXME comment

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lgtm-com bot commented Apr 3, 2021

This pull request introduces 2 alerts when merging 9c1c496 into 113407f - view on LGTM.com

new alerts:

  • 2 for FIXME comment

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drroe commented Apr 3, 2021

@swails I'm seeing a lot of docker-related failures with Jenkins this morning. Is this something that will likely clear up if I try later?

@drroe drroe merged commit 56f1ae0 into Amber-MD:master Apr 4, 2021
@drroe drroe deleted the addGistPme branch April 4, 2021 13:24
@drroe drroe mentioned this pull request Apr 6, 2021
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