thomassedlmeyr / psemoldyn_groupg

An efficient simulation software for molecules programmed in C++ from scratch

Description

This project was part of a practical course on molecular dynamics at TU Munich (IN0012). Based on a template provided at TUM-I5/MolSim. For this project we implemented several algorithms for example the Linked Cell Algorithm and evaluated the results. All generated videos can be found here: https://youtube.com/playlist?list=PLHRoJMZN0Kf06ifBcb74CIgupYphcu4IW

Members:

• Thomas Sedlmeyr
• Philip Haitzer
• Daniel Braun

Run Instructions

Standard Run of default input file

• compile with all options
• run ./MolSim
• see in the following section on how to change the xml-file to your liking

Run with own xml file

• compile with all options

• run with the input flag

  • -h : help page
  • -input : provides path to xml input file

• example runs:

  • ./MolSim -input ../src/XML_Parser/input.xml

• xml-file must be formatted correctly according to schema

• you can use and change the default file in ../src/XML_Parser/input.xml

  • generalParams :
    • t_end : specifies end time of simulation
    • delta_t : specifies stepsize for calculation
    • writeFrequency : specifies the write frequency
    • dimensionType : 2D or 3D as Type for simulation
    • parallelType : you can choose from two parallel types (first, second, notParallel)
    • g_grav : gravitational force (0 if not used)
    • useGravity : yes or no
    • gravDirection : direction of gravitational force
    • calcType : G for Gravitation Simulation, LJ for LennardJones Simulation
    • baseNameOutputFiles : specifies the output name
    • cutoffRadius : corresponding calculated cuttoff radius for linked cells algorithm
    • gravInput : path to input file for Gravitation Simulation, can otherwise be left blank
    • loadCheckpoint : yes or no
    • makeCheckpoint : yes or no
    • pathInCheckpoint : path for input checkpoint file
    • pathOutCheckpoint : path for file to write output checkpoints
    • domainSizeX, domainSizeY, domainSizeZ : domain size of corresponding coordinates
    • thermostatType : different types of thermostats (regular, only fluid)
    • useThermostat : yes or no
    • useBrownianMotion : yes or no (for initialisation with brownian motion)
    • T_init : initial temperature
    • T_target : target temperature
    • delta_T : max temperature difference in one scaling step
    • n_thermostat : time steps after which thermostat is applied periodically
    • useVelDensProfiling : create CSV file every 1000 iterations about density and velocity downwards (not possible to be used with Gravitation simulation)
    • numberOfBins : number of bins that the domain is supposed to be grouped into (greater 0)
    • pathToAnalysisFolder : path to folder for analysis files
    • crystallization_r_c : only to be set for crystallization
    • crystallization_r_l : only to be set for crystallization *boundaryConditions:
    • top, right, bottom, left, front, back : outflowType, reflectingType, betterReflectingType or periodicType
  • particles : specify as many bodies as needed here
    • body :
      • bodyType : Cuboid, Sphere, Tetrahedron, Membrane
      • position : initial position
      • velocity : initial velocity
      • objectSpecificFormat :
        • for Cuboid : particles per dimension, e.g. "8,8,1"
        • for Tetrahedron : numberParticles per edge, e.g. "15"
        • for Sphere : radius, e.g. "10"
        • for Membrane : e.g. "n_50,50,1 r_2.2 k_300 f_0.8 p_(17,24),(17,25),(18,24),(18,25) t_150"
          • obligatory : n, r, k
          • optional : f, p, t (when there is no lifting, all must be omitted then)
          • n : number of particles per dimension
          • r : average bond length of molecule pair (double)
          • k : stiffness constant (double)
          • f : force lifting membrane (double)
          • p : points to be lifted (coordinates, see example)
          • t : time for lifting to last for (int)
      • epsilon : value for epsilon
      • mass : value for mass
      • rho : value for rho
      • h : mesh width of grid
      • bodyState : moving, fixed (membrane must be moving)

• optional : when performing a Gravitation Simulation

  • other tags in generalParams and boundaryConditions can all be put to 0, particlesLJ can be left empty

Run with predefined xml-files

Run of Gravitation Simulation

• compile with all options
• run ./MolSim -input ../XMLinputFiles/Gravitation.xml
• alternatively you can change the default xml file
  • switch calcType to G
  • set gravInput to the input file path ../eingabe-sonne.txt
    • for additional planets specify the path ../eingabe-sonnen_system.txt

Run of 'Simulation of a falling drop - Wall'

• compile with all options
• 2D Mode: run ./MolSim -input ../XMLinputFiles/FallingRaindropWall_2D.xml
• 3D Mode: run ./MolSim -input ../XMLinputFiles/FallingRaindropWall_3D.xml

Run of 'Collision of two bodies'

• compile with all options
• run ./MolSim -input ../XMLinputFiles/CollisionOfTwoBodies.xml

Run of 'Simulation of the Rayleigh-Taylor instability'

• compile with all options
• run ./MolSim -input ../XMLinputFiles/RayleighTaylor_(small|large).xml

Run of 'Simulation of a falling drop - Liquid Part 1'

• compile with all options
• run ./MolSim -input ../XMLinputFiles/FallingDropLiquid_makeCheckpoint.xml
• creates Checkpoint which can be used for Part 2

Run of 'Simulation of a falling drop - Liquid Part 2'

• compile with all options
• run ./MolSim -input ../XMLinputFiles/FallingDropLiquid_loadCheckpoint.xml

Run of 'Simulation of the Rayleigh-Taylor instability'

• compile with all options
• run on of the following
  • run ./MolSim -input ../XMLinputFiles/RayleighTaylor_3D.xml
  • run ./MolSim -input ../XMLinputFiles/RayleighTaylor_large.xml
  • run ./MolSim -input ../XMLinputFiles/RayleighTaylor_small.xml

Run of 'Simulation of a membrane'

• compile with all options
• run ./MolSim -input ../XMLinputFiles/Membrane.xml

Run of 'Nano-scale flow simulation'

• compile with all options
• run ./MolSim -input ../XMLinputFiles/NanoScaleFlow.xml

Run of 'Crystallization of Argon'

• compile with all options
• for equilibration
  • run ./MolSim -input ../XMLinputFiles/Crystallization_equilibrate.xml
• for cooling
  • run ./MolSim -input ../Crystallization_cooling.xml
  • run ./MolSim -input ../Crystallization_supercooling.xml

Crating a doxygen

• compile with BUILD_DOXYGEN=ON
• run make doc_doxygen

Execute Tests

• compile with all options
• run make or make Tests
• run ctest in build directory

Media

Videos

• [Animation of the Membrane] (https://youtu.be/yGJPIwb_p5c)
• [Rayleigh Taylor 3D] (https://youtu.be/6lqAMLsCMuI)
• [Cooling Argon] (https://youtu.be/H75T12H-Yig)
• [Super Cooling Argon] (https://youtu.be/P0fYduY6CYk)
• [Extra Nano Flow Simulations] (https://youtu.be/lVIDD30yHl8) (https://youtu.be/gRUX0L14Klg) (https://youtu.be/BeIFKaWc6MI)