From b4be4bcedbeefec84e21adc11377aa7a84a6184e Mon Sep 17 00:00:00 2001 From: VasiliBaranov Date: Tue, 16 May 2017 20:11:55 +0200 Subject: [PATCH] Equilibration (-md) description changed. --- README.md | 29 +++++++++++++++++++---------- 1 file changed, 19 insertions(+), 10 deletions(-) diff --git a/README.md b/README.md index c549550..be57bcd 100644 --- a/README.md +++ b/README.md @@ -91,7 +91,7 @@ little-endian format. > Seed: 341
> Steps to write: 1000
> Boundaries mode: 1
-> Contraction rate: 1.328910e-005
+> Contraction rate: 1.328910e-002
> Generation mode: 1
> 1. boundaries mode: 1 - bulk; 2 - ellipse (inscribed in XYZ box, Z is length of an ellipse); 3 - rectangle
> 2. generationMode = 1 (Poisson, R) or 2 (Poisson in cells, S)
@@ -279,12 +279,13 @@ They are saved in a binary file *insertion_radii.txt* (as floating point numbers in double precision in little-endian byte order). 2. -entropy [optional integer to specify min radii count]: calculates the "pore-size entropy" at once by -the formula (12) from *Baranau et al (2013) Pore-size entropy of random hard-sphere packings*, +the formula (12) from *Baranau et al. (2013) Pore-size entropy of random hard-sphere packings*, [doi:10.1039/C3SM27374A](http://pubs.rsc.org/en/content/articlelanding/2013/sm/c3sm27374a). The factor alpha is chosen as 2. The radii count is selected dynamically, so that adding 10000 pores changes the large pores quantity by no more than 1%. Optional integer will specify min pores quantity to generate, it's 1e7 by default (therefore computation will consume several minutes). Entropy is -saved in a file *entropy.txt* (not as a binary float, just a simple text value). +saved in a file *entropy.txt* (not as a binary float, just a simple text value). See also +*Baranau and Tallarek (2016)*, [doi:10.1063/1.4953079](http://aip.scitation.org/doi/full/10.1063/1.4953079). 3. -directions: calculates all unique directions between particles (uses closest periodic images for directions), saves it to a text file *particle_directions.txt*. It has five columns: zero-based @@ -293,7 +294,7 @@ first particle center to the second particle center (of unity length). 4. -contraction: calculates energies of particle intersections after uniform packing contraction (or, equivalently, radii increases), as if particles were supplied with potential. Uses second-order -harmonic potential (see *Xu et. al. (2005) Random close packing revisited: Ways to pack frictionless +harmonic potential (see *Xu et al. (2005) Random close packing revisited: Ways to pack frictionless disks*, [doi:10.1103/PhysRevE.71.061306](http://link.aps.org/doi/10.1103/PhysRevE.71.061306)) and zero-order potential which is equivalent to calculating coordination number per particle. For jammed packings coordination number should be close to 6. Results are saved into a text file @@ -306,13 +307,21 @@ removal see option -rm below. *Jin, Makse (2010) A first-order phase transition defines the random close packing of hard spheres*, [doi:10.1016/j.physa.2010.08.010](http://www.sciencedirect.com/science/article/pii/S0378437110006928). -6. -md: conducts Lubachevscky-Stillinger simulation with zero contraction rate, i.e., molecular -dynamics simulation, tracks reduced pressure, waits until packings are completely equilibrated -(pressure is stationary) and saves stationary pressure into a text file +6. -md [optional integer to specify number of LS steps]: conducts Lubachevscky-Stillinger simulation +with zero contraction rate, i.e., molecular dynamics simulation. It tracks the reduced pressure, +self-diffusion coefficient, full intermediate scattering function (ISF), +and self-part of the ISF. Terminates when the pressure changes sufficiently slowly *and* +the normalized full ISF crosses the critical value *e-1* at least ten times. +The optional integer specifies the number of LS steps (each step is 20 collisions per particle). +Some computed parameters are displayd in stdout as a log (thus, one can use *-md | tee log.txt*). +Scattering function values are saved in the *ScatteringFunctions* folder. +For more advanced options, refer to the source code +([MolecularDynamicsStatistics.cpp, CalculateStationaryStatistics](https://github.com/VasiliBaranov/packing-generation/blob/master/PackingGeneration/Generation/PackingServices/PostProcessing/Source/MolecularDynamicsService.cpp#L117)). +At the end, saves the stationary reduced pressure into a text file *molecular_dynamics_statistics.txt*. You can supply this stationary pressure into the equation of -state by Salsburg and Wood. See *Salsburg and Wood (1962) Equation of State of Classical Hard Spheres -at High Density*, [doi:10.1063/1.1733163](http://jcp.aip.org/resource/1/jcpsa6/v37/i4/p798_s1). -The results of this application by me are not yet submitted anywhere. +state by Salsburg and Wood, if packing was close enough to jamming. +See *Salsburg and Wood (1962) Equation of State of Classical Hard Spheres +at High Density*, [doi:10.1063/1.1733163](http://jcp.aip.org/resource/1/jcpsa6/v37/i4/p798_s1). 7. -rm: removes rattler particles. Particle is a rattler if it has less than 4 contacts if the packing is uniformely contracted with a strain rate 1e-7. Rattlers are removed recursively (because