Configuration Files for `htpolynet postsim`¶

postsim is a subcommand that provides for convenient post-build MD simulations for annealing, equilibration, and making measurements of properties, like Young’s modulus and glass transition temperature. Its main advantage is that it understands the project file system structure and uses many sensible default values, making it easy to run post-build MD simulations.

A postsim configuration file is written in YAML and structured as a list of dictionaries, each entry of which is a stage which together constitute a sequence of stages. Each stage involves an MD simulation for which you can specify the input coordinates and mdp parameters. Because postsim executes a sequence of stages, the output of one stage can be the input for a later stage.

HTPolyNet recoginizes the following types of post-build MD simulations

Simulation Type	keyword	Description
Equilibration	`equilibrate`	Plain MD in NVT or NPT
Annealing	`anneal`	Temperature annealing using a low T and a high T and a schedule for cycling between them
Temperature-ladder	`ladder`	Controlled change in T from one temperature to another over some number of stages of some duration
Uniaxial deformation	`deform`	Uniaxial strain at a constant rate in one direction for a specified duration

Equilibration directives

An equilibrate directive allows specification of several parameters:

Keyword	Description
`subdir`	Name of directory in which simulation is conducted relative to the project directory default: `postsim/equilibrate`
`input_top`	Input topology file relative to the project directory; default: `systems/final-results/final.top`
`input_gro`	Input coordinate file relative to the project directory; default: `systems/final-results/final.gro`
`input_grx`	Input extended atom attribute file relative to the project directory; default: `systems/final-results/final.grx`
`output_deffnm`	default gromacs output file basename; default: `equilibrate`
`traces`	List of trace types to generate output files for
`scatter`	Tuple specifying a scatter plot to generate based on the traces
`gromacs`	Gromacs directives; see here
`T`	Temperature in K default: 300
`P`	Pressure in bar default: 1
`ps`	Duration of simulation in picoseconds; default: 1000

A minimal post-build equilibration file for 100 ns at 310 K and 5 bar would contain:

- equilibrate:
    ps: 100000
    T: 310
    P: 5

Here, it uses the topology and coordinate files at the end of the build, and runs for 100 ns, with the results in <proj-dir>/postsim/equilibrate. Notice the - character at the left-most indent level; this indicates that the file is a list of items; the indentation of ps: indicates it that the identifier equilibrate is a keyword whose value is a dictionary.

Traces

postsim provides a shortcut approach to using gmx energy to extract energy-like quantities from Gromacs energy file (edr). For example, if we would like to extract traces of temperature and density:
```
- equilibrate:
    ps: 1000
    traces:
      - Temperature
      - Density
```
Note we have to list the names of the energy-like quantities exactly how gmx energy reports them.
Scatter plots

postsim also provides a shortcut interface to matplotlib to generate simple trace plots of any quantity extracted using traces. The single argument of the scatter keyword is a tuple in which the first element is the name of the x-data (typically time(ps)), the second is a list of names of energy-like quantities to trace (e.g., [Density, Temperature]), and the third element is the name of an output image file to contain the plot.

We can add a scatter directive thusly
```
- equilibrate:
    ps: 1000
    T: 310
    P: 5
    traces:
      - Temperature
      - Density
    scatter:
      - time(ps)
      - - Density
        - Temperature
      - my_plot.png
```
Running postsim

Suppose we put the YAML shown above into the file eq.yml. To use this input configuration to launch a new post-build equilibration in the project directory proj-1, one would issue the command
```
htpolynet postsim -cfg eq.yml -proj proj-1 -ocfg <build.cfg>
```
The -ocfg key identifies the YAML config file used for the actual build; postsim extracts some information about the monomer library and other inputs from here; it also uses the Gromacs configuration of the original build config unless overridded in the postsim config.

Annealing

Annealing simulations are useful to help in densifying amorphous systems; the idea is that cycles of heating and cooling help the atoms fall deeper into local potential energy wells. It is usually a good idea to anneal a newly built system before measuring any properties.

An anneal directive allows specification of several parameters:

Keyword	Description
`subdir`	Name of directory in which simulation is conducted relative to the project directory default: `postsim/anneal`
`input_top`	Input topology file relative to the project directory; default: `systems/final-results/final.top`
`input_gro`	Input coordinate file relative to the project directory; default: `systems/final-results/final.gro`
`input_grx`	Input extended atom attribute file relative to the project directory; default: `systems/final-results/final.grx`
`output_deffnm`	default gromacs output file basename; default: `equilibrate`
`traces`	List of trace types to generate output files for
`scatter`	Tuple specifying a scatter plot to generate based on the traces
`gromacs`	Gromacs directives; see here
`P`	Pressure (bar)
`ncycles`	number of annealing cycles
`T0`	“low” temperature
`T1`	“high” temperature
`T0_to_T1_ps`	duration of T-change simulation for T0 to T1 in ps
`T1_ps`	duration of T-hold at T1 in ps
`T1_to_T0_ps`	duration of T-change simulaiton for T1 to T0 in ps
`T0_ps`	duration of T-hold at T0 in ps (completing a cycle)

An example anneal postsim directive might look like:

- anneal:
    input_top: 'systems/final-results/final.top'
    input_gro: 'systems/final-results/final.gro'
    P: 1
    T0: 300
    T1: 600
    ncycles: 3
    T0_to_T1_ps: 10000
    T1_ps: 10000
    T1_to_T0_ps: 10000
    T0_ps: 10000

Temperature ladders

Temperature-ladder simulations are useful in the response of system density to temperature over a wide temperature domain. This can be useful for estimating the coefficient of thermal expansion and the glass transition temperature.

A ladder directive allows specification of several parameters:

Keyword	Description
`subdir`	Name of directory in which simulation is conducted relative to the project directory default: `postsim/anneal`
`input_top`	Input topology file relative to the project directory; default: `systems/final-results/final.top`
`input_gro`	Input coordinate file relative to the project directory; default: `systems/final-results/final.gro`
`input_grx`	Input extended atom attribute file relative to the project directory; default: `systems/final-results/final.grx`
`output_deffnm`	default gromacs output file basename; default: `equilibrate`
`traces`	List of trace types to generate output files for
`scatter`	Tuple specifying a scatter plot to generate based on the traces
`gromacs`	Gromacs directives; see here
`P`	Pressure (bar)
`Tlo`	“low” temperature (K)
`Thi`	“high” temperature (K)
`deltaT`	change in temperature between subsequent simulations on the ladder
`ps_per_rise`	duration (ps) of T-change simulation beginning a new step on the ladder
`ps_per_run`	duration (ps) of T-hold simulation at each step
`warmup_ps`	duration (ps) of a warmup simulation before beginning T-changes

An example ladder postsim directive might look like:

- ladder:
    input_top: 'systems/final-results/final.top'
    input_gro: 'postsim/equilibrate/equilibrate.gro'
    subdir: 'postsim/ladder-heat'
    Tlo: 300
    Thi: 600
    deltaT: 5
    ps_per_rise: 100
    ps_per_run: 900
    warmup_ps: 1000

One can go either up or down a ladder. If deltaT is specified as a postive number, the initial temperature is Tlo. However, if deltaT is specified as a negative number, the intial temperature is Thi instead of Tlo. One way I like to use ladders is as one big cycle, measuring thermal response in both directions:

- ladder:
    input_top: 'systems/final-results/final.top'
    input_gro: 'postsim/equilibrate/equilibrate.gro'
    subdir: 'postsim/ladder-heat'
    Tlo: 300
    Thi: 600
    deltaT: 5
    ps_per_rise: 100
    ps_per_run: 900
    warmup_ps: 1000
- ladder:
    input_top: 'systems/final-results/final.top'
    input_gro: 'postsim/ladder-heat/ladder.gro'
    subdir: 'postsim/ladder-cool'
    Tlo: 300
    Thi: 600
    deltaT: -5
    ps_per_rise: 100
    ps_per_run: 900
    warmup_ps: 1000

A measure of how well equilibrated your system is and how carefully you conducted the ladder simulations is agreement between the thermal responses in the T-up and T-down ladders.

By default, a ladder generates a trace of both temperature and density from the associated edr files. The plots subcommand can be used to read these files for a set of equivalent project directories and compute a glass transition temperature.

Uniaxial deformation

Constant strain-rate uniaxial deformation MD simulations can be performed using postsim as well. Such simulations are used to generate stress-strain curves from which moduli are extracted.

A deform directive allows specification of several parameters:

Keyword	Description
`subdir`	Name of directory in which simulation is conducted relative to the project directory default: `postsim/anneal`
`input_top`	Input topology file relative to the project directory; default: `systems/final-results/final.top`
`input_gro`	Input coordinate file relative to the project directory; default: `systems/final-results/final.gro`
`input_grx`	Input extended atom attribute file relative to the project directory; default: `systems/final-results/final.grx`
`output_deffnm`	default gromacs output file basename; default: `equilibrate`
`traces`	List of trace types to generate output files for
`scatter`	Tuple specifying a scatter plot to generate based on the traces
`gromacs`	Gromacs directives; see here
`direction`	Direction along with strain is applied; x, y, or z
`edot`	Dimensionless strain rate in ps^-1; 0.0001 = 10⁸ s^-1
`ps`	Duration of the simulation in ps; product of `ps` and `edot` gives the strain at the end of the simulation.

An example deform postsim directive might look like:

- deform:
    input_top: 'systems/final-results/final.top'
    input_gro: 'postsim/equilibrate/equilibrate.gro'
    subdir: 'postsim/deform-x'
    direction: x
    edot: 0.0001
    ps: 1000  # final strain 10%

For isotropic (bulk) systems, the x, y, and z directions are equivalent, and one should measure material response along all three directions. One can use a single input configuration file to stipulate all three such simulations, each starting from a common initial condition:

- deform:
    input_top: 'systems/final-results/final.top'
    input_gro: 'postsim/equilibrate/equilibrate.gro'
    subdir: 'postsim/deform-x'
    direction: x
    edot: 0.0001
    ps: 1000  # final strain 10%
- deform:
    input_top: 'systems/final-results/final.top'
    input_gro: 'postsim/equilibrate/equilibrate.gro'
    subdir: 'postsim/deform-y'
    direction: y
    edot: 0.0001
    ps: 1000  # final strain 10%
- deform:
    input_top: 'systems/final-results/final.top'
    input_gro: 'postsim/equilibrate/equilibrate.gro'
    subdir: 'postsim/deform-z'
    direction: z
    edot: 0.0001
    ps: 1000  # final strain 10%

By default, a deform block generates a traces of normal stress tensor components along the pulling direction and box size along that direction. This allows the plots subcommand to estimate Young’s modulus.

Configuration Files for `htpolynet postsim`¶

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Configuration Files for htpolynet postsim¶

Configuration Files for `htpolynet postsim`¶