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Merge pull request #2721 from agiliopadua/examples

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New examples for FEP calculation and references in doc pages
This commit is contained in:
Axel Kohlmeyer
2021-04-30 12:55:57 -04:00
committed by GitHub
parent b7fb28f940 85ba1e9e3b
commit 8d8158396f
31 changed files with 6438 additions and 0 deletions
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2
doc/src/Howto_drude2.rst
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@ -9,6 +9,8 @@ USER-DRUDE package activated. Then, the data file and input scripts
have to be modified to include the Drude dipoles and how to handle
them.
Example input scripts available: examples/USER/drude
----------
**Overview of Drude induced dipoles**

2
doc/src/compute_fep.rst
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@ -48,6 +48,8 @@ Examples
compute 1 all fep 298 pair lj/cut epsilon 1 * v_delta pair lj/cut sigma 1 * v_delta volume yes
compute 1 all fep 300 atom charge 2 v_delta
Example input scripts available: examples/USER/fep
Description
"""""""""""

2
doc/src/compute_temp_drude.rst
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@ -20,6 +20,8 @@ Examples
compute TDRUDE all temp/drude
Example input scripts available: examples/USER/drude
Description
"""""""""""

3
doc/src/fix_adapt_fep.rst
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@ -56,6 +56,9 @@ Examples
fix 1 all adapt/fep 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes
fix 1 all adapt/fep 10 atom diameter 1 v_size
Example input scripts available: examples/USER/fep
Description
"""""""""""

2
doc/src/fix_drude.rst
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@ -22,6 +22,8 @@ Examples
fix 1 all drude 1 1 0 1 0 2 2 2
fix 1 all drude C C N C N D D D
Example input scripts available: examples/USER/drude
Description
"""""""""""

2
doc/src/fix_drude_transform.rst
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@ -25,6 +25,8 @@ Examples
fix 3 all drude/transform/direct
fix 1 all drude/transform/inverse
Example input scripts available: examples/USER/drude
Description
"""""""""""

2
doc/src/fix_langevin_drude.rst
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@ -35,6 +35,8 @@ Examples
fix 3 all langevin/drude 300.0 100.0 19377 1.0 20.0 83451
fix 1 all langevin/drude 298.15 100.0 19377 5.0 10.0 83451 zero yes
Example input scripts available: examples/USER/drude
Description
"""""""""""

2
doc/src/fix_tgnh_drude.rst
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@ -62,6 +62,8 @@ Examples
fix 2 jello tgnpt/drude temp 300.0 300.0 100.0 1.0 20.0 tri 5.0 5.0 1000.0
fix 2 ice tgnpt/drude temp 250.0 250.0 100.0 1.0 20.0 x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000
Example input scripts available: examples/USER/drude
Description
"""""""""""

1
doc/src/pair_coul_tt.rst
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@ -29,6 +29,7 @@ Examples
pair_coeff 1 2 coul/tt 4.0 1.0 4 12.0
pair_coeff 1 3* coul/tt 4.5 1.0 4
Example input scripts available: examples/USER/drude
Description
"""""""""""

2
doc/src/pair_fep_soft.rst
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@ -182,6 +182,8 @@ Examples
pair_coeff * * 100.0 2.0 1.5 1.0
pair_coeff 1 1 100.0 2.0 1.5 1.0 3.0
Example input scripts available: examples/USER/fep
Description
"""""""""""

2
doc/src/pair_thole.rst
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@ -42,6 +42,8 @@ Examples
pair_style lj/cut/thole/long 2.6 12.0
Example input scripts available: examples/USER/drude
Description
"""""""""""