Tutorial 0

This tutorial will introduce you to running molecular dynamics on ground states in presto.

Introduction

For each trajectory, presto requires both a config file and a checkpoint file.

A config file contains information about the run: how the forces will be computed, the desired temperature, runtime, and so forth. Config files are agnostic to molecular structure and can be recycled for many different trajectories; they are written in the .yaml format and are easily editable by hand.

A checkpoint file contains the masses, positions, forces, and accelerations of individual atoms at each timestep. Checkpoint files are written in the .hdf5 format and are not human-readable. If your run is very long, the checkpoint file may grow to several gigabytes or more! To begin a new run, either an .xyz geometry or a previous checkpoint file must be supplied to initialize the new checkpoint file.

Here, we will run molecular dynamics on a single benzene molecule using GFN2-xtb.

The config file (test.yaml) is shown here:

  # presto config file
  type: equilibration
  timestep: 1
  stop_time: 250
  anchor: 1

  integrator:
      type: langevin
      viscosity: 0.0001

  calculator:
      type: xtb
      gfn : 2
      parallel: 8

  bath_scheduler:
      type: constant
      target_temp: 298

This config file tells presto several important facts:

This is an "equilibration" trajectory, not a "reaction" trajectory, so we don't need to check to see if a reaction is done.
The timestep will be 1 fs, and the trajectory will run for 250 fs in total.
Atom #1 is "anchored" to the origin by a weak harmonic potential.
We will use the Langevin integrator to control temperature, with a viscosity of 0.0001 Pascal-seconds (a reasonable default).
We will use GFN2-xtb to compute forces, using 8 processors.
We will set the temperature to a constant 298 K (no gradual heating/cooling).

We also need a starting geometry (benzene.xyz):

  12
  benzene
  C                 -3.00142242   -0.33428165    0.00000000
  C                 -1.60626242   -0.33428165    0.00000000
  C                 -0.90872442    0.87346935    0.00000000
  C                 -1.60637842    2.08197835   -0.00119900
  C                 -3.00120342    2.08190035   -0.00167800
  C                 -3.69880442    0.87369435   -0.00068200
  H                 -3.55118142   -1.28659865    0.00045000
  H                 -1.05675442   -1.28679465    0.00131500
  H                  0.19095558    0.87354935    0.00063400
  H                 -1.05617842    3.03412135   -0.00125800
  H                 -3.55132542    3.03418135   -0.00263100
  H                 -4.79840842    0.87387735   -0.00086200

Finally, we need an actual script to load and run our trajectory (test_presto.py):

  import logging, presto
  logging.basicConfig(level=logging.INFO, filename=f"test.log", format='%(asctime)s %(name)-12s  %(message)s', datefmt='%m-%d %H:%M')

  traj = presto.config.build("test.yaml", "test.chk", geometry="benzene.xyz")
  print("Built trajectory...")
  traj.run(checkpoint_interval=25)
  print("Trajectory finished!")

Here, we initialize the logging module so we can monitor the progress of our trajectory at test.log. We then initialize a presto.trajectory.Trajectory object from test.yaml and benzene.xyz, creating test.chk in the process. Finally, we run our trajectory, saving to test.chk every 25 frames.

Running

This script should only take 1-2 minutes to run. After it finishes, you can see two new files:

  (presto) [tutorial00]$ ls
  benzene.xyz  presto.config  test_presto.py  test.yaml
  (presto) [tutorial00]$ python test_presto.py
  Built trajectory...
  Trajectory finished!
  (presto) [tutorial00]$ ls
  benzene.xyz  presto.config  test.chk  test.log  test_presto.py  test.yaml
  (presto) [tutorial00]$ cat test.log
  11-28 14:24 presto.trajectory  Initializing new equilibration trajectory...
  11-28 14:24 presto.trajectory  Saving trajectory to new checkpoint file test.chk (1 frames)
  11-28 14:24 presto.trajectory  Loaded trajectory from checkpoint file test.chk -- 1 frames read.
  11-28 14:24 presto.trajectory  Propagating trajectory.
  11-28 14:24 presto.trajectory  Saving trajectory to existing checkpoint file test.chk (25 frames added; 26 in total)
  11-28 14:24 presto.trajectory  Saving trajectory to existing checkpoint file test.chk (25 frames added; 51 in total)
  11-28 14:24 presto.trajectory  Saving trajectory to existing checkpoint file test.chk (25 frames added; 76 in total)
  11-28 14:24 presto.trajectory  Saving trajectory to existing checkpoint file test.chk (25 frames added; 101 in total)
  11-28 14:25 presto.trajectory  Saving trajectory to existing checkpoint file test.chk (25 frames added; 126 in total)
  11-28 14:25 presto.trajectory  Saving trajectory to existing checkpoint file test.chk (25 frames added; 151 in total)
  11-28 14:25 presto.trajectory  Saving trajectory to existing checkpoint file test.chk (25 frames added; 176 in total)
  11-28 14:25 presto.trajectory  Saving trajectory to existing checkpoint file test.chk (25 frames added; 201 in total)
  11-28 14:25 presto.trajectory  Saving trajectory to existing checkpoint file test.chk (25 frames added; 226 in total)
  11-28 14:25 presto.trajectory  Saving trajectory to existing checkpoint file test.chk (24 frames added; 250 in total)
  (presto) [tutorial00]$

If you see a logfile like this, presto has successfully completed the trajectory!

Analysis

You can analyze the checkpoint file using scripts/analyze.py. (Run python analyze.py --help to view script options.)

  (presto) [tutorial00]$ cp ../../scripts/analyze.py .
  (presto) [tutorial00]$ python analyze.py -c 0 -m all test.yaml test.chk
  250 frames loaded from test.chk (250 total)
  trajectory finished!
  TEMPERATURE:		374.54 K (± 93.13)
    599.87  ┤                             ╭╮
    573.65  ┤                             ││
    547.44  ┤                             │╰╮╭╮
    521.22  ┤                       ╭╮╭╮  │ ╰╯│
    495.01  ┤                       │╰╯╰╮ │   │            ╭╮   ╭╮
    468.79  ┤                      ╭╯   │╭╯   │  ╭╮╭╮      ││   ││
    442.57  ┤          ╭╮ ╭──╮     │    ╰╯    │  ││││      │╰─╮ ││ ╭╮
    416.36  ┤        ╭╮││ │  │    ╭╯          │  ││││  ╭─╮ │  │ ││ ││              ╭╮
    390.14  ┤        ││││╭╯  ╰─╮  │           │  │╰╯╰─╮│ │ │  │ ││ │╰─╮            ││   ╭╮   ╭╮
    363.92  ┤      ╭─╯╰╯╰╯     ╰╮ │           ╰╮╭╯    ╰╯ │ │  ╰─╯╰╮│  ╰╮           ││╭╮ │╰╮  ││
    337.71  ┼╮     │            │╭╯            ││        ╰╮│      ╰╯   │ ╭╮╭─╮ ╭─╮╭╯╰╯│ │ ╰╮ ││
    311.49  ┤│ ╭╮ ╭╯            ╰╯             ││         ╰╯           ╰─╯││ │ │ ││   ╰─╯  │ ││
    285.27  ┤│ │╰╮│                            ││                         ││ │ │ ││        ╰╮││
    259.06  ┤│ │ ╰╯                            ╰╯                         ╰╯ ╰╮│ ╰╯         ││╰
    232.84  ┤│ │                                                              ╰╯            ╰╯
    206.62  ┤╰╮│
    180.41  ┤ ╰╯
    154.19  ┤
  ENERGY:			-15.86 (± 2.68 kcal/mol)
  -9946.49  ┤                                 ╭╮
  -9947.26  ┤                           ╭╮    │╰╮
  -9948.03  ┤                           ││    │ │
  -9948.80  ┤                           ││    │ │        ╭╮               ╭╮
  -9949.57  ┤                          ╭╯╰╮   │ ╰╮       ││      ╭╮      ╭╯│
  -9950.34  ┤         ╭─╮              │  │   │  │╭─╮    ││   ╭─╮││      │ │
  -9951.11  ┤         │ ╰─╮     ╭╮     │  ╰─╮╭╯  ╰╯ ╰╮  ╭╯│   │ ││╰╮╭╮   │ │
  -9951.88  ┤         │   │     │╰╮    │    ││       │  │ │  ╭╯ ╰╯ ╰╯│  ╭╯ │        ╭╮
  -9952.65  ┤        ╭╯   │    ╭╯ ╰─╮  │    ││       ╰╮╭╯ ╰╮ │       │ ╭╯  │   ╭──╮ │╰─╮
  -9953.42  ┤    ╭╮  │    │    │    │ ╭╯    ╰╯        ││   │ │       │ │   ╰╮  │  │ │  ╰╮ ╭─╮
  -9954.19  ┤  ╭─╯╰╮ │    ╰─╮  │    ╰╮│               ╰╯   │ │       ╰╮│    │╭─╯  ╰─╯   │ │ │
  -9954.95  ┤  │   │╭╯      │╭─╯     ╰╯                    │╭╯        ╰╯    ╰╯          │ │ ╰╮
  -9955.72  ┤╭─╯   ╰╯       ╰╯                             ╰╯                           │ │  │
  -9956.49  ┤│                                                                          ╰╮│  │
  -9957.26  ┤│                                                                           ╰╯  │
  -9958.03  ┤│                                                                               ╰─
  -9958.80  ┼╯
  -9959.57  ┤
  writing movie to test.pdb...

Here, we can see that the temperature and energy fluctuate a lot initially but gradually approach the desired value. 250 fs is not very long, and a longer trajectory would permit better equilibration. (As a bulk property, temperature is also prone to fluctuation on a system this small.)

The movie (test.pdb) can be viewed using any trajectory viewer (e.g. Avogadro), and shows the expected combination of vibrational modes.

Congratulations! You have completed your first presto trajectory!