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Combined USER-FEP related updates #1302

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merged 29 commits into from Jan 31, 2019

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@akohlmey
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akohlmey commented Jan 24, 2019

Purpose

Combine pull requests related to adding "soft" class2 styles to USER-FEP and consolidating/updating the documentation of all "soft" pair styles in a consistent way in a single file.

closes #1300
closes #1293
closes #1289
closes #1269

this also removes references in the entire documentation of pre-installed packages.

Author(s)

Evangelos Voyiatzis
Agilio Padua, ENS de Lyon
Axel Kohlmeyer (ICTP)

Backward Compatibility

For pair styles buck/mdf and lennard/mdf the extract-able parameters have been renamed to be consistent with other similar potentials (aparm/bparm/cparm was renamed to a/b/c)

evoyiatzis and others added some commits Jan 9, 2019

files for soft lj/class2 potentials
the source code for the three soft core class2 potentials
Update Install.sh
Addition of the six files for the class 2 potentials in the end of Install.sh
Updating the list of potentials in fix_adapt_fep.txt
There are several potentials that contain the method extract() but they are not included in the "fix adapt" and "fix adapt/fep"
A small update of the list is attempted here. The same potentials might be added to the documentation of fix_adapt if it is useful.
Merge branch 'core_soft' of https://github.com/agiliopadua/lammps int…
…o combined-user-fep-soft-updates

Resolved Conflicts:
	doc/src/compute_fep.txt
	doc/src/fix_adapt_fep.txt
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agiliopadua left a comment

Thank you. I was fixing the links too.
I've added the new lj/class2/soft entries to Commands_pair.txt and to pair_style.txt
Just pushed a commit.

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akohlmey commented Jan 24, 2019

Thank you. I was fixing the links too.
I've added the new lj/class2/soft entries to Commands_pair.txt and to pair_style.txt
Just pushed a commit.

can't merge anything from that PR anymore, since i had to make some changes to correct spelling and improve consistency. but i've updated the lists of pair styles. fixing the links was done with a single "sed" command, so no big deal there. it looked worse in the jenkins report, than it actually was. So please check, if this is still missing something. thanks.

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agiliopadua commented Jan 24, 2019

Looks good, thanks!

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agiliopadua commented Jan 25, 2019

I've improved the evaluation of the approximation in the tail corrections to energy and virial. Could you add the change below?

diff --git a/doc/src/pair_fep_soft.txt b/doc/src/pair_fep_soft.txt
index 864aebded..06781d07f 100644
--- a/doc/src/pair_fep_soft.txt
+++ b/doc/src/pair_fep_soft.txt
@@ -319,13 +319,14 @@ interaction.

NOTE: The analytical form of the tail corrections for energy and pressure used
in the {lj/cut/soft} potentials are approximate, being identical to that of the
-corresponding non-soft potentials scaled by a factor lambda^n. For real-space
-cutoffs greater than 2.5 sigma and alpha_LJ = 0.5, the error affecting the tail
-correction is below 0.2% when lambda = 0 (worse case). This error disappears as
-lambda approaches 1. Note that this is the error affecting the long-range tail
-(itself a correction to the interaction energy) which includes other
-approximations, namely that the system is homogenous (local density equal the
-average density) beyond the cutoff.
+corresponding non-soft potentials scaled by a factor lambda^n. The errors due to
+this approximation should be negligible. For example, for a cutoff of 2.5 sigma
+this approximation leads to maximum relative errors in tail corrections of the
+order of 1e-4 for energy and virial (alpha_LJ = 0.5, n = 2). The error vanishes
+when lambda approaches 0 or 1. Note that these are the errors affecting the
+long-range tail (itself a correction to the interaction energy) which includes
+other approximations, namely that the system is homogenous (local density equal
+the average density) beyond the cutoff.

The {morse/soft} pair style does not support the "pair_modify"_pair_modify.html
tail option for adding long-range tail corrections to energy and pressure.

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akohlmey commented Jan 25, 2019

I've improved the evaluation of the approximation in the tail corrections to energy and virial. Could you add the change below?

the diff/patch here seems to be truncated. would you mind, to submit the change as pull request to
the branch combined-user-fep-soft-updates in my LAMMPS fork at https://github.com/akohlmey/lammps/ ?

or e-mail me a complete (and gzipped) patch?

thanks,
axel.

agiliopadua and others added some commits Jan 25, 2019

Merge branch 'core_soft' of https://github.com/agiliopadua/lammps int…
…o combined-user-fep-soft-updates

Resolved Conflicts:
	doc/src/Commands_pair.txt
	doc/src/pair_fep_soft.txt
	doc/src/pair_style.txt
	doc/src/pairs.txt

@akohlmey akohlmey requested a review from stanmoore1 Jan 30, 2019

Show resolved Hide resolved doc/src/pair_fep_soft.txt Outdated
Show resolved Hide resolved src/USER-FEP/pair_lj_class2_soft.h Outdated

@akohlmey akohlmey merged commit 7606529 into lammps:master Jan 31, 2019

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@akohlmey akohlmey deleted the akohlmey:combined-user-fep-soft-updates branch Feb 1, 2019

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