Documentation of VV, NPT, Thermostats #2939

christophlohrmann · 2019-06-25T07:14:25Z

Fixes #2680

Description of changes:

Added sphinx documentation for velocity verlet, NPT
Added/Updated sphinx documentation for Langevin, NPT, LB, DPD thermostat
Found some papers as reference

PR Checklist

Tests?
- Interface
- Core
Docs?

doc/sphinx/inter_non-bonded.rst

KaiSzuttor · 2019-06-25T07:26:42Z

doc/sphinx/lb.rst

+with a single position  ``pos`` as an argument can be used. 
+For the GPU fluid :class:`espressomd.lb.LBFluidGPU`
+also :py:attr:`espressomd.lb.LBFluidGPU.get_interpolated_fluid_velocity_at_positions()`
+is available, which expects a numpy array of positions as an argument.


could you please also mention the issue of interpolating velocities near boundaries?

codecov · 2019-06-25T07:49:54Z

Codecov Report

Merging #2939 into python will decrease coverage by <1%.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           python   #2939    +/-   ##
=======================================
- Coverage      83%     82%    -1%     
=======================================
  Files         520     519     -1     
  Lines       26746   26958   +212     
=======================================
- Hits        22328   22312    -16     
- Misses       4418    4646   +228

Impacted Files	Coverage Δ
src/core/electrostatics_magnetostatics/mmm1d.cpp	`31% <0%> (-64%)`	⬇️
src/core/nonbonded_interactions/thole.hpp	`75% <0%> (-25%)`	⬇️
src/core/specfunc.cpp	`58% <0%> (-24%)`	⬇️
...e/electrostatics_magnetostatics/coulomb_inline.hpp	`89% <0%> (-6%)`	⬇️
src/core/virtual_sites/VirtualSitesRelative.cpp	`81% <0%> (-4%)`	⬇️
src/core/electrostatics_magnetostatics/coulomb.cpp	`78% <0%> (-1%)`	⬇️
src/core/communication.cpp	`94% <0%> (-1%)`	⬇️
src/core/electrostatics_magnetostatics/p3m.cpp	`85% <0%> (-1%)`	⬇️
src/core/grid_based_algorithms/lb_interface.cpp	`74% <0%> (-1%)`	⬇️
src/core/cells.cpp	`90% <0%> (-1%)`	⬇️
... and 39 more

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doc/sphinx/inter_non-bonded.rst

jonaslandsgesell · 2019-06-25T09:48:27Z

doc/sphinx/system_setup.rst


 The keyword ``seed`` controls the state of the random number generator (Philox
 Counter-based RNG) and is required on first activation of the thermostat. It
 can be omitted in subsequent calls of ``set_langevin()``. It is the user's
 responsibility to decide whether the thermostat should be deterministic (by
 using a fixed seed) or not (by using a randomized seed).

+The diffusion coeffictient :math:`D` of the particle can be obtained by the Einstein-Smoluchowski relation


We should discuss to what degree the plain Einstein-Smoluchowski relation is applicable to the gamma which is set in the thermostat. In my mind what is presented in the text only holds for ideal systems. Interactions in the system will modify the DIffusion coefficient -- otherwise there would never be a need to measure diffusion coefficients using the mean squared displacement or a green kubo formula in MD simulations.

I agree with @jonaslandsgesell, the documentation should not make statements about the diffusion coefficient here.

@jonaslandsgesell I would remove the mention of the diffusion coefficient entirely, as @fweik suggested.

Hey Christoph. Why not removing it?yes, I mean for ideal (noninteracting ) particles one should observe D=kT/gamma_thermostat. So we state that gamma is the friction of the thermostat somewhere?

We say that gamma is the bare friction coefficient for the Langevin equation and any physics beyond that should be the user's responsibility.

Sounds good!

christophlohrmann · 2019-06-25T14:03:18Z

Concerning the dimensions enabled/disabled for scaling in the NPT algorithm:

The corresponding code has not been touched since the original commit from 2004.
The author (Ira Cooke) did not describe this method in any of his papers and I cannot
find his dissertation on the Max Planck homepage. Also I did not find any other paper
using that method.

Should I just mark that option as not tested and leave it like that?

jngrad · 2019-07-16T08:12:56Z

mark NPT as experimental and update "Usage Status = None" in:
https://github.com/espressomd/espresso/blob/python/doc/sphinx/introduction.rst#available-simulation-methods

RudolfWeeber

bors r+

jngrad · 2019-07-25T11:01:10Z

bors r-

bors · 2019-07-25T11:02:58Z

Canceled

RudolfWeeber · 2019-07-25T11:05:13Z

I checked NPT against Monte Carlo volume moves. It seems to work, in principle.

The PR improves the docs alot. I'd suggest not to defer much longer and instead open a new pr if there is something to add.

jngrad · 2019-07-25T14:02:26Z

bors r=RudolfWeeber

2939: Documentation of VV, NPT, Thermostats r=RudolfWeeber a=christophlohrmann Fixes #2680 Description of changes: - Added sphinx documentation for velocity verlet, NPT - Added/Updated sphinx documentation for Langevin, NPT, LB, DPD thermostat - Found some papers as reference PR Checklist ------------ - [ ] Tests? - [ ] Interface - [ ] Core - [x] Docs? 3006: Reduce usage of local cells r=fweik a=KaiSzuttor Fixes part of #2899 Description of changes: - replacement for #2991 3008: Removed from __future__ r=jngrad a=jrfinkbeiner Fixes #3004 3015: Update checkpointing docs r=jngrad a=RudolfWeeber Fixes #2808 Co-authored-by: Christoph Lohrmann <clohrmann@icp.uni-stuttgart.de> Co-authored-by: Jean-Noël Grad <jgrad@icp.uni-stuttgart.de> Co-authored-by: Kai Szuttor <kai@icp.uni-stuttgart.de> Co-authored-by: Alexander Reinauer <st144434@stud.uni-stuttgart.de> Co-authored-by: Jan Finkbeiner <st144298@stud.uni-stuttgart.de> Co-authored-by: Rudolf Weeber <weeber@icp.uni-stuttgart.de>

bors · 2019-07-25T19:47:36Z

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bors · 2019-07-25T19:47:36Z

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2939: Documentation of VV, NPT, Thermostats r=RudolfWeeber a=christophlohrmann Fixes #2680 Description of changes: - Added sphinx documentation for velocity verlet, NPT - Added/Updated sphinx documentation for Langevin, NPT, LB, DPD thermostat - Found some papers as reference PR Checklist ------------ - [ ] Tests? - [ ] Interface - [ ] Core - [x] Docs? 3006: Reduce usage of local cells r=fweik a=KaiSzuttor Fixes part of #2899 Description of changes: - replacement for #2991 Co-authored-by: Christoph Lohrmann <clohrmann@icp.uni-stuttgart.de> Co-authored-by: Jean-Noël Grad <jgrad@icp.uni-stuttgart.de> Co-authored-by: Kai Szuttor <kai@icp.uni-stuttgart.de> Co-authored-by: Alexander Reinauer <st144434@stud.uni-stuttgart.de>

bors · 2019-07-25T21:26:46Z

Build succeeded

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bors · 2019-07-25T22:28:10Z

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bors · 2019-07-25T22:28:35Z

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christophlohrmann added 4 commits June 13, 2019 17:50

VV and LD explained, no papers yet

6e3b086

found some refs

350ad4c

DPD, NPT, LB now with references

9f745c5

NPT direction, typo

cf45b9f

KaiSzuttor reviewed Jun 25, 2019

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christophlohrmann added 2 commits June 25, 2019 10:26

DPD temp, lb interp bounds, sphinx :meth:

f233b4a

langevin: rem diffusion coeff

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jonaslandsgesell reviewed Jun 25, 2019

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reintroduced diffusion coeff, removed ref

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KaiSzuttor added this to the Espresso 4.1 milestone Jul 15, 2019

RudolfWeeber approved these changes Jul 25, 2019

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doc: marked NPT as experimental, rem diff coeff (again)

47494fe

Merge branch 'python' into 2680_vv_docu

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bors bot merged commit e64e5f7 into espressomd:python Jul 25, 2019

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Documentation of VV, NPT, Thermostats #2939

Documentation of VV, NPT, Thermostats #2939

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Documentation of VV, NPT, Thermostats #2939

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