Note that this tutorial is under construction and subject to changes.
Basics of Minima Hopping: Minima Hopping on a Mg7 cluster
The purpose of this lesson is to get familiar with basic variables needed to run a Minima Hopping calculation on a cluster. At the end of the lesson, one will be able to prepare the inputs required for an efficient production run and understand the important part of the output. This lesson may take 2 hours. If you have already finished the tutorial and facing some problems during the Minima Hopping run see troubleshooting section.
In this tutorial we assume that the user is already familiar with basic BigDFT inputs. We will use the Mg7 cluster as an example system in this tutorial.
File Structure Overview
- input.yaml: same as the input file in case of BigDFT. It is recommended to use the SQNM optimizer in the geometry section.
- mdinput.yaml: same format as input.yaml but but contains lower accuracy parameters. It is recommended to use the SQNM optimizer in the geometry section.
- poscur.xyz: Input coordinates for the starting configuration.
- psppar.XX : the pseudo-potential file. See BigDFT manual for explanations.
- rand.inp: contains a single integer value which is used as seed to generate random numbers for MD part.
- disable_hatrans: If present, principle axis transformations are disabled. This is essential if the output of MH should be used for MHGPS. The disable_hatrans file must contains a number that determines after how many accepted configuration MH should stop.
These files are updated during the run.
- enarr: This file contains the energy of all the local minima found in the system. The file has the following structure.
9 19 # of minima already found, # of minima to be found in consecutive run 0.30000000000000000E-02 0.30000000000000000E-02 en_delta, fp_delta 0.50929999999999997E+00 5.0000000000E+00 0.51510000000000000E+00 6.0000000000E+00 0.51610000000000000E+00 1.0000000000E+00 0.51724999999999999E+00 7.0000000000E+00 0.51775000000000004E+00 4.0000000000E+00 0.52980000000000005E+00 1.0000000000E+00 0.55049999999999999E+00 1.0000000000E+00 0.55710000000000004E+00 1.0000000000E+00 0.55890000000000006E+00 1.0000000000E+00
The first line contains two integer numbers indicating the number of minima already found and the number of minima to be found in future run. For a new run the 1st number is " 0 " . The second line is en_delta and fp_delta: The energy and fingerprint thresholds used to identify identical confugurations. From the foruth line on the file contains the sorted energies of local minima and the number of times each minimum is visited. So in this example file the energy of the global minima is 0.50929999999999997E+00 and it has been visited 5 times during the run.
- ioput: This file contains four parameters: ediff, ekinetic, dt and nsoften. Follow the tutorial to know how to adjust these parameters.
7.32050000000000149E-03 3.70012497212908811E-02 7.10681330130121025E-01 10 ediff ekinetic dt nsoften
Besides the standard output and the BigDFT output files, there are two further output files of the Minima Hopping code.
- poslow******.xyz: The coordinates of the local minima found in the system. poslow000001.xyz is the global minimum.poslow000002.xyz is 1st local minimum.
- posacc******.xyz: The sequence of accepted minima along the MH
- global.mon: A log file of all the minima visited.