.. _pms_results:
Results
-------
Overall behavior
^^^^^^^^^^^^^^^^
Using ``htpolynet plots`` we can generate a few interesting graphics that help characterize a build. In this tutorial, we generated a 95%-cure build under ``proj-0``, with diagnostic output in ``diagnostics.log`` and console output to ``console.log``.
As an exercise, copy ``pMSTY.yaml`` to ``pMSTY-low.yaml`` and in it, change the desired cure to 0.50 instead of 0.95. Then launch a second build:
.. code-block:: bash
$ htpolynet run -diag diagnostics-low.log pMSTY-low.yaml &> console-low.log
This will populate the project directory ``proj-1`` (whose name is automatically assigned). Once it completes, we can generate some plots.
First, we can make plots of the conversion vs. run time and the cure iteration vs. run time:
.. code-block:: console
$ htpolynet plots diag --diags diagnostics.log diagnostics-low.log
This generates ``cure_info.png``:
.. figure:: pics/cure_info.png
(Left) Conversion vs. wall-clock time; (right) Iteration number vs wall-clock time.
We can see here that the 95\% cure took about 8 and a half minutes of run time (which is not really impressive since this is a **very** small system). Fully two-thirds of the run time is consumed realizing the final 15\% of the cure.
Second, we can make plots that track the temperature, density, and potential energy throughout the entire build process:
.. code-block:: console
$ htpolynet plots build --proj proj-0 --buildplot t --traces t d p
This command extracts temperature, density, and potential energy from all Gromacs ``edr`` output files in ``proj-0/`` in the order they were generated, plots them according to a default format, and stores the extracted data in a ``csv`` file. By default, the plot is in ``proj-0/buildtraces.png`` and the corresponding data in ``proj-0/buildtraces.csv``.
.. figure:: pics/buildtraces.png
(Top) Temperature vs. run time; (middle) Density vs. run time; (bottom) Potential energy vs. run time. In all panels, vertical lines designate initiations of Gromacs simulations.
From these traces, we can see how little MD time is actually devoted to forming the bonds as compared to relaxing both before and after. The top plot shows temperature in K vs. time in ps througout the build process. Vertical lines denote transitions from one step to the next; transitions are very close together in time during the CURE iterations since I'm showing one transition for each drag/relax stage. The middle plot shows the density trace' note how the density begins at the stipulated low value of 300 kg/m3\ :sup:`3`\. The bottom plot shows the potential energy trace.
In the figure below, we show two renderings of this system. In each, all bonds between C1 and C2 atoms are shown as grey tubes, and all other bonds are colored by individual unique monomer and made transparent. On the left is the system just after the precure anneal, where you can see that only **intramolecular** C1 and C2 bonds exist. On the right is the system after postcure, where you can see chains of -C1-C2- bonds.
.. list-table::
* - .. figure:: pics/hi-pre.png
Methystyrene liquid before cure.
- .. figure:: pics/hi.png
Poly(methyl styrene) after 95% cure.
Details
^^^^^^^
The ``htpolynet run`` invocation in ``run.sh`` runs a high-cure build (95\% conversion) in the ``proj-0`` subdirectory, generating and populating the following directory structure:
.. code-block:: console
$ cd proj-0
$ tree -d .
.
├── lib
│ └── molecules
│ ├── inputs
│ └── parameterized
└── proj-0
├── molecules
│ └── parameterized
├── plots
└── systems
├── capping
├── densification
├── final-results
├── init
├── iter-1
├── iter-10
├── iter-11
├── iter-12
├── iter-13
├── iter-2
├── iter-3
├── iter-4
├── iter-5
├── iter-6
├── iter-7
├── iter-8
├── iter-9
├── postcure
└── precure
There are three main subdirectories in all project directories:
* ``molecules/``: This directory has one subdirectory, ``molecules/parameterized`` that contains all files associated with generation and parameterization of all molecules and oligomer templates. The important files here are those with ``gro``, ``top``, ``itr``, ``tpx``, and ``grx`` extensions.
* ``systems/``: This directory contains all directories where Gromacs runs are conducted.
* ``plots/``: This directory contains some plots generated on the fly.
``proj-0/systems``
~~~~~~~~~~~~~~~~~~
The ``init/`` directory is where the initial topology and coordinates are generated.
.. code-block:: console
$ ls systems/init
EMB.gro init.gro init.grx init.top
Then in ``densification`` are the files associated with the MD simulations used to densify the initial system.
.. code-block:: console
$ ls systems/densification
densified-min.edr densified-npt.edr densified-nvt.edr init.grx
densified-min.gro densified-npt.gro densified-nvt.gro init.top
densified-min.log densified-npt.log densified-nvt.log init.tpx
densified-min.mdp densified-npt.mdp densified-nvt.mdp mdout.mdp
densified-min.tpr densified-npt.tpr densified-nvt.tpr min.mdp
densified-min.trr densified-npt.trr densified-nvt.trr npt.mdp
densified-npt.cpt densified-nvt.cpt init.gro nvt.mdp
The files with ``init`` basenames are copied from the ``systems/init`` directory. You can note output from three separate Gromacs ``mdrun`` invocations: 1. a minimization; 2. an NVT equilibration, and 3. an NPT equilibration.
Next comes the ``precure`` directory, which contains all the results of the precure equilibrations and annealing (if requested).
.. code-block:: console
$ ls systems/precure
annealed.cpt postequilibration-npt.edr
annealed.edr postequilibration-npt.gro
annealed.gro postequilibration-npt.log
annealed.log postequilibration-npt.mdp
annealed.tpr postequilibration-npt.tpr
annealed.trr postequilibration-npt.trr
densified-npt.gro preequilibration-npt.cpt
init.grx preequilibration-npt.edr
init.top preequilibration-npt.gro
init.tpx preequilibration-npt.log
mdout.mdp preequilibration-npt.mdp
npt.mdp preequilibration-npt.tpr
nvt.mdp preequilibration-npt.trr
postequilibration-npt.cpt
Here, ``init.top``, ``init.tpx``, and ``init.grx`` are copied from ``systems/densification``, as is coordinate file ``densified-npt.gro``. These are input to the pre-annealing equilibration (``preequilibration-npt.*``), which then serves as input to the annealing simulation (``annealed.*``), which in turn serves as input to the post-annealing equilibration (``postequilibration-npt.*``).
Next come the iteration directories; here, thirteen CURE iterations were run. Below we show just a listing of the ``iter-1`` directory.
.. code-block:: console
$ ls systems/iter-1
0-cure_bondsearch-bonds.csv 3-cure_relax-stage-1-nvt.tpr 3-cure_relax-stage-3-min.tpr 3-cure_relax-stage-4-npt.tpr 3-cure_relax-stage-5-nvt.tpr
2-cure_update-bonds.csv 3-cure_relax-stage-1-nvt.trr 3-cure_relax-stage-3-min.trr 3-cure_relax-stage-4-npt.trr 3-cure_relax-stage-5-nvt.trr
2-cure_update.gro 3-cure_relax-stage-1.top 3-cure_relax-stage-3-npt.cpt 3-cure_relax-stage-4-nvt.cpt 3-cure_relax-stage-5.top
2-cure_update.grx 3-cure_relax-stage-2-min.edr 3-cure_relax-stage-3-npt.edr 3-cure_relax-stage-4-nvt.edr 4-cure_equilibrate-npt.cpt
2-cure_update-idx-mapper.csv 3-cure_relax-stage-2-min.gro 3-cure_relax-stage-3-npt.gro 3-cure_relax-stage-4-nvt.gro 4-cure_equilibrate-npt.edr
2-cure_update.top 3-cure_relax-stage-2-min.log 3-cure_relax-stage-3-npt.log 3-cure_relax-stage-4-nvt.log 4-cure_equilibrate-npt.gro
2-cure_update.tpx 3-cure_relax-stage-2-min.tpr 3-cure_relax-stage-3-npt.tpr 3-cure_relax-stage-4-nvt.tpr 4-cure_equilibrate-npt.log
3-cure_relax-complete.top 3-cure_relax-stage-2-min.trr 3-cure_relax-stage-3-npt.trr 3-cure_relax-stage-4-nvt.trr 4-cure_equilibrate-npt.mdp
3-cure_relax-relax-bonds.csv 3-cure_relax-stage-2-npt.cpt 3-cure_relax-stage-3-nvt.cpt 3-cure_relax-stage-4.top 4-cure_equilibrate-npt.tpr
3-cure_relax-stage-1-min.edr 3-cure_relax-stage-2-npt.edr 3-cure_relax-stage-3-nvt.edr 3-cure_relax-stage-5-min.edr 4-cure_equilibrate-npt.trr
3-cure_relax-stage-1-min.gro 3-cure_relax-stage-2-npt.gro 3-cure_relax-stage-3-nvt.gro 3-cure_relax-stage-5-min.gro init.grx
3-cure_relax-stage-1-min.log 3-cure_relax-stage-2-npt.log 3-cure_relax-stage-3-nvt.log 3-cure_relax-stage-5-min.log init.top
3-cure_relax-stage-1-min.tpr 3-cure_relax-stage-2-npt.tpr 3-cure_relax-stage-3-nvt.tpr 3-cure_relax-stage-5-min.tpr init.tpx
3-cure_relax-stage-1-min.trr 3-cure_relax-stage-2-npt.trr 3-cure_relax-stage-3-nvt.trr 3-cure_relax-stage-5-min.trr linkcell-0.50.grx
3-cure_relax-stage-1-npt.cpt 3-cure_relax-stage-2-nvt.cpt 3-cure_relax-stage-3.top 3-cure_relax-stage-5-npt.cpt mdout.mdp
3-cure_relax-stage-1-npt.edr 3-cure_relax-stage-2-nvt.edr 3-cure_relax-stage-4-min.edr 3-cure_relax-stage-5-npt.edr npt.mdp
3-cure_relax-stage-1-npt.gro 3-cure_relax-stage-2-nvt.gro 3-cure_relax-stage-4-min.gro 3-cure_relax-stage-5-npt.gro postequilibration-npt.gro
3-cure_relax-stage-1-npt.log 3-cure_relax-stage-2-nvt.log 3-cure_relax-stage-4-min.log 3-cure_relax-stage-5-npt.log relax-min.mdp
3-cure_relax-stage-1-npt.tpr 3-cure_relax-stage-2-nvt.tpr 3-cure_relax-stage-4-min.tpr 3-cure_relax-stage-5-npt.tpr relax-npt.mdp
3-cure_relax-stage-1-npt.trr 3-cure_relax-stage-2-nvt.trr 3-cure_relax-stage-4-min.trr 3-cure_relax-stage-5-npt.trr relax-nvt.mdp
3-cure_relax-stage-1-nvt.cpt 3-cure_relax-stage-2.top 3-cure_relax-stage-4-npt.cpt 3-cure_relax-stage-5-nvt.cpt
3-cure_relax-stage-1-nvt.edr 3-cure_relax-stage-3-min.edr 3-cure_relax-stage-4-npt.edr 3-cure_relax-stage-5-nvt.edr
3-cure_relax-stage-1-nvt.gro 3-cure_relax-stage-3-min.gro 3-cure_relax-stage-4-npt.gro 3-cure_relax-stage-5-nvt.gro
3-cure_relax-stage-1-nvt.log 3-cure_relax-stage-3-min.log 3-cure_relax-stage-4-npt.log 3-cure_relax-stage-5-nvt.log
Files in iteration directories are prepended with a number that corresponds to their order. Here we have files that begin with 0, 2, and 3. "0" refers to the initial search for possible bonds; these are reported in the ``csv`` file. "1" (which is missing here) refers to pre-bond dragging; since no new bonds were longer than 0.8 nm, pre-bond dragging was not triggered. "2" refers to the generation of the new bonded topology. "3" refers to post-bond-formation relaxation to allow new bonds to relax to their equilibrium lengths. These relaxations progress through five iterations of minimization-NVT-NPT simulations to relax the new bonds.
Some CURE iterations may require pre-bond dragging. In the system I ran to generate this documentation, no cases of prebond dragging were required.
Then comes the ``capping`` directory where the final topology updates are performed to cap any unreacted monomers (reverting them from their "active" forms to their "proper" forms). In this run, this directory is empty, since no unreacted monomers exist at the end of the CURE.
Then comes ``postcure`` equilibration and relaxation.
.. code-block:: console
$ ls systems/postcure
2-cure_update.grx mdout.mdp
2-cure_update.tpx npt.mdp
3-cure_relax-complete.top nvt.mdp
4-cure_equilibrate-npt.gro postequilibration-npt.cpt
annealed.cpt postequilibration-npt.edr
annealed.edr postequilibration-npt.gro
annealed.gro postequilibration-npt.log
annealed.log postequilibration-npt.mdp
annealed.tpr postequilibration-npt.tpr
annealed.trr postequilibration-npt.trr
The files beginning with digits are copied either from the last ``iter`` directory or the ``capping`` directory (here, since no capping was necessary, they came from ``iter-13``). As stipulated in the configuration file, we first run annealing, and then a post-annealing NPT equilibration.
Finally, HTPolyNet copies the results of the postcure, with new file names, into ``final-results``.
.. code-block:: console
$ ls final-results
final.gro final.grx final.top final.tpx
Here we see the ``top``, ``gro``, ``tpx``, and ``grx`` files of the final system; the ``top`` and ``gro`` files can be used right away for Gromacs MD simulations.
``proj-0/plots``
~~~~~~~~~~~~~~~~
``HTPolyNet`` generates several plots on the fly during a system build.
.. code-block:: console
$ ls plots
densification-density.png
iter-10-cure_equilibrate-density.png
iter-11-cure_equilibrate-density.png
iter-12-cure_equilibrate-density.png
iter-13-cure_equilibrate-density.png
iter-1-cure_equilibrate-density.png
iter-2-cure_equilibrate-density.png
iter-3-cure_equilibrate-density.png
iter-4-cure_equilibrate-density.png
iter-5-cure_equilibrate-density.png
iter-6-cure_equilibrate-density.png
iter-7-cure_equilibrate-density.png
iter-8-cure_equilibrate-density.png
iter-9-cure_equilibrate-density.png
postcure-anneal-T.png
postcure-postequilibration-density.png
precure-anneal-T.png
precure-postequilibration-density.png
precure-preequilibration-density.png
reaction_network.png
For example, ``densification-density.png`` indicates that the densification simulation was in fact able to densify the system:
.. figure:: pics/densification-density.png
``densification-density.png`` for the high-cure build of polymethylstyrene.
We can check that the annealing cycles were correctly performed from ``precure-anneal-T.png`` ``postcure-anneal-T.png``:
.. list-table::
* - .. figure:: pics/precure-anneal-T.png
Temperature during pre-cure annealing.
- .. figure:: pics/postcure-anneal-T.png
Temperature during post-cure annealing.
Finally, we can take a look at the density after the postcure-anneal in ``postcure-postequilibration-density.png``:
.. figure:: pics/postcure-postequilibration-density.png
``postcure-postequilibration-density.png``
Density during post-cure annealing of the 95% cured system.
Note that the final equilibrated density at 300 K and 1 bar is about 935 kg/m\ :sup:`3`\. This is quite a bit higher than the density of liquid styrene at 10 bar and 300 K from the densification simulations (about 800 kg/m\ :sup:`3`\). However, this result is outside the range expected for `poly(4-methyl styrene) <https://polymerdatabase.com/polymers/poly4-methylstyrene.html>`_ of about 1.01 g/cc, but it's not too suprising given that this is a very small system with a low molecular weight, and it was not very extensively equilibrated.