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Parallelism on images, the string method

String method for the computation of minimum energy paths, in parallel.

This tutorial aims at showing how to use the parallelism on images, by performing a calculation of a minimum energy path (MEP) using the string method.

You will learn how to run the string method on a parallel architecture and what are the main input variables that govern convergence and numerical efficiency of the parallelism on images. Other algorithms use images, e.g. path-integral molecular dynamics, hyperdynamics, linear combination of images, … with different values of ionmov. The parallelism on images can be used for all these algorithms.

You are supposed to know already some basics of parallelism in ABINIT, explained in the tutorial A first introduction to ABINIT in parallel, and ground state with plane waves.

This tutorial should take about 1.5 hour and requires to have at least a 10 CPU core parallel computer.

Note

Supposing you made your own installation of ABINIT, the input files to run the examples are in the ~abinit/tests/ directory where ~abinit is the absolute path of the abinit top-level directory. If you have NOT made your own install, ask your system administrator where to find the package, especially the executable and test files.

In case you work on your own PC or workstation, to make things easier, we suggest you define some handy environment variables by executing the following lines in the terminal:

export ABI_HOME=Replace_with_absolute_path_to_abinit_top_level_dir # Change this line
export PATH=$ABI_HOME/src/98_main/:$PATH      # Do not change this line: path to executable
export ABI_TESTS=$ABI_HOME/tests/             # Do not change this line: path to tests dir
export ABI_PSPDIR=$ABI_TESTS/Psps_for_tests/  # Do not change this line: path to pseudos dir

Examples in this tutorial use these shell variables: copy and paste the code snippets into the terminal (remember to set ABI_HOME first!) or, alternatively, source the set_abienv.sh script located in the ~abinit directory:

source ~abinit/set_abienv.sh

The ‘export PATH’ line adds the directory containing the executables to your PATH so that you can invoke the code by simply typing abinit in the terminal instead of providing the absolute path.

To execute the tutorials, create a working directory (Work*) and copy there the input files of the lesson.

Most of the tutorials do not rely on parallelism (except specific tutorials on parallelism). However you can run most of the tutorial examples in parallel with MPI, see the topic on parallelism.

1 Summary of the String Method

The string method [Weinan2002] is an algorithm that allows the computation of a Minimum Energy Path (MEP) between an initial (i) and a final (f) configuration. It is inspired from the Nudge Elastic Band (NEB) method. A chain of configurations joining (i) to (f) is progressively driven to the MEP using an iterative procedure in which each iteration consists of two steps:

  1. Evolution step: the images are moved following the atomic forces.
  2. Reparametrization step: the images are equally redistributed along the string.

The algorithm presently implemented in ABINIT is the so-called simplified string method [Weinan2007]. It has been designed for the sampling of smooth energy landscapes.

Before continuing you might work in a different subdirectory as for the other tutorials. Why not work_paral_images?

Important

In what follows, the names of files are mentioned as if you were in this subdirectory. All the input files can be found in the \$ABI_TESTS/tutoparal/Input directory. You can compare your results with reference output files located in \$ABI_TESTS/tutoparal/Refs.

In the following, when “run ABINIT over nn CPU cores” appears, you have to use a specific command line according to the operating system and architecture of the computer you are using. This can be for instance: mpirun -n nn abinit input.abi or the use of a specific submission file.

Tip

In this tutorial, most of the images and plots are easily obtained using the post-processing tool qAgate or agate, its core engine. Any post-process tool will work though !!

2 Computation of the initial and final configurations

We propose to compute the energy barrier for transferring a proton from an hydronium ion (H3O+) onto a NH3 molecule:

\begin{equation} \nonumber \rm H_3O^+ + NH_3 \rightarrow H_2O + NH_4^+ \end{equation}

Starting from an hydronium ion and an ammoniac molecule, we obtain as final state a water molecule and an ammonium ion NH4+. In such a process, the MEP and the barrier are dependent on the distance between the hydronium ion and the NH3 molecule. Thus we choose to fix the O atom of H3O+ and the N atom of NH3 at a given distance from each other (4.0 Å = 7.5589 bohr). The calculation is performed using a LDA exchange-correlation functional.

You can visualize the initial and final states of the reaction below (H atoms are in white, the O atom is in red and the N atom in blue).

initial state

final state

Tip

To obtain these images, open the timages_01.abi and timages_02.abi files with agate or qAgate

Before using the string method, it is necessary to optimize the initial and final points. The input files timages_01.abi and timages_02.abi contain respectively two geometries close to the initial and final states of the system. You have first to optimize properly these initial and final configurations, using for instance the Broyden algorithm implemented in ABINIT.

Open the timages_01.abi file and look at it carefully. The unit cell is defined at the begining. Note that the keywords natfix and iatfix are used to keep fixed the positions of the O and N atoms. The cell is tetragonal and its size is larger along x so that the periodic images of the system are separated by 4.0 Å (7.5589 bohr) of vacuum in the three directions. The keyword cellcharge is used to remove an electron of the system and thus obtain a protonated molecule (neutrality is recovered by adding a uniform compensating charge background).

Although this input file will run on a single core, the paral_kgb keyword is set to 1 to activate the LOBPCG [Bottin2008] algorithm. Note the use of bandpp 10 to accelerate the convergence.

Important

If your system were larger and required more CPU time, all the usual variables for parallelism npkpt, npband, npfft, npspinor could be used wisely.

Then run the calculation in sequential, first for the initial configuration (timages_01.abi), and then for the final one (timages_02.abi). You should obtain the following positions:

  1. for the initial configuration:

    xcart      0.0000000000E+00  0.0000000000E+00  0.0000000000E+00
              -7.1119330966E-01 -5.3954252784E-01  1.6461078895E+00
              -7.2706367116E-01  1.6395559231E+00 -5.3864186404E-01
               7.5589045315E+00  0.0000000000E+00  0.0000000000E+00
               8.2134747935E+00 -1.8873337293E-01 -1.8040045499E+00
               8.1621251369E+00 -1.4868515614E+00  1.0711027413E+00
               8.2046046694E+00  1.6513534511E+00  7.5956562273E-01
               1.9429112745E+00  4.2303909125E-02  2.9000318893E-02
    
  2. for the final configuration:

    xcart      0.0000000000E+00  0.0000000000E+00  0.0000000000E+00
              -5.8991482730E-01 -3.6948430331E-01  1.7099330811E+00
              -6.3146217793E-01  1.6964706443E+00 -3.6340264832E-01
               7.5589045315E+00  0.0000000000E+00  0.0000000000E+00
               8.4775515860E+00 -2.9286989031E-01 -1.6949564152E+00
               7.9555913454E+00 -1.4851844626E+00  1.1974660442E+00
               8.2294855730E+00  1.6454040992E+00  8.0048724879E-01
               5.5879660323E+00  1.1438061815E-01 -2.5524007156E-01
    

Once you have properly optimized the initial and final states of the process, you can turn to the computation of the MEP. Let us first have a look at the related keywords.

imgmov

Selects an algorithm using replicas of the unit cell. For the string method, choose 2.

nimage

gives the number of replicas of the unit cell including the initial and final ones.

dynimage(nimage)

arrays of flags specifying if the image evolves or not (0: does not evolve; 1: evolves).

ntimimage

gives the maximum number of iterations (for the relaxation of the string).

tolimg

convergence criterion (in Hartree) on the total energy (averaged over the nimage images).

fxcartfactor

“time step” (in Bohr2/Hartree) for the evolution step of the string method. For the time being (ABINITv6.10), only steepest-descent algorithm is implemented.

npimage

gives the number of processors among which the work load over the image level is shared. Only dynamical images are considered (images for which dynimage is 1). This input variable can be automatically set by ABINIT if the number of processors is large enough.

prtvolimg

governs the printing volume in the output file (0: full output; 1: intermediate; 2: minimum output).

4 Computation of the MEP without parallelism over images

You can now start with the string method. First, for test purpose, we will not use the parallelism over images and will thus only perform one step of string method.

Open the timages_03.abi file and look at it. The initial and final configurations are specified at the end through the keywords xcart and xcart_lastimg. By default, ABINIT generates the intermediate images by a linear interpolation between these two configurations. In this first calculation, we will sample the MEP with 12 points (2 are fixed and correspond to the initial and final states, 10 are evolving). nimage is thus set to 12. The npimage variable is not used yet (no parallelism over images) and ntimimage is set to 1 (only one time step).

Since the parallelism over the images is not used, this calculation still runs over 1 CPU core.

5 Computation of the MEP using parallelism over images

Now you can perform the complete computation of the MEP using the parallelism over the images.

Open the timages_04.abi file. The keyword npimage has been added and set to 10, and ntimimage has been increased to 50. This calculation has thus to be run over 10 CPU cores.

The convergence of the string method algorithm is controlled by tolimg, which has been set to 0.0001 Ha. In order to obtain a more lisible output file, you can decrease the printing volume and set prtvolimg to 2. Then run ABINIT over 10 CPU cores.

When the calculation is completed, ABINIT provides you with 12 configurations that sample the Minimum Energy Path between the initial (i) and final (f) states. Plotting the total energy of these configurations with respect to a reaction coordinate that join (i) to (f) gives you the energy barrier that separates (i) from (f). In our case, a natural reaction coordinate can be the distance between the hopping proton and the O atom of H2O (dOH), or equivalently the distance between the proton and the N atom (dHN). The graph below shows the total energy as a function of the OH distance along the MEP. It indicates that the barrier for crossing from H2O to NH3 is ~1.36 eV. The 6th image gives an approximate geometry of the transition state. Note that in the initial state, the OH distance is significantly stretched, due to the presence of the NH3 molecule.

Tip

Note that the total energy of each of the 12 replicas of the simulation cell can be found at the end of the output file in the section:

-outvars: echo values of variables after computation  --------
The total energies are printed out as: etotal_1img, etotal_2img, ...., etotal_12img.

Tip

Also, you can can have a look at the atomic positions in each image: in cartesian coordinates (xcart_1img, xcart_2img, …) or in reduced coordinates (xred_1img, xred_2img, …) to compute the OH distance.

Tip

You can issue the command :plot xy x="distance 1 8 dunit=A" y="etotal eunit=eV" in agate or qAgate

courbe 1

Total energy as a function of OH distance for the path computed with 12 images

and tolimg=0.0001 (which is very close to the x coordinate of the proton: first coordinate of xcart for the 8th atom in the output file).

The keyword npimage can be automatically set by ABINIT if autoparal is set to 1.

Let us test this functionality. Edit again the timages_04.abi file and comment the npimage line, then add autoparal=1. Then run the calculation again over 10 CPU cores.

Open the output file and look at the npimage value …

6 Converging the MEP

Like all physical quantities, the MEP has to be converged with respect to some numerical parameters. The two most important are the number of points along the path (nimage) and the convergence criterion (tolimg).

  1. nimage

    Increase the number of images to 22 (2 fixed + 20 evolving) and recompute the MEP. Don’t forget to update dynimage to 0 20*1 0 ! And you have 20 CPU cores available then set npimage to 20 and run ABINIT over 20 CPU cores. The graph below superimposes the previous MEP (grey curve, calculated with 12 images) and the new one obtained by using 22 images (cyan curve). You can see that the global profile is almost not modified as well as the energy barrier.

    curve 2

    Total energy as a function of OH distance for the path computed with 12 images and tolimg=0.0001 (grey curve) and the one computed with 22 images and tolimg=0.0001 (red curve).

    Tip

    The image can be obtained with agate or qagate with the following commands

    :open timages_04_MPI10o_HIST.nc # 12 images calculation
    :plot xy x="distance 1 8 dunit=A" y="etotal eunit=eV" hold=true
    :open timages_04_MPI10_22o_HIST.nc # 22 images calculation
    :plot xy x="distance 1 8 dunit=A" y="etotal eunit=eV"
    
    Replace plot with print to get the gnuplot script.

    The following animation is made by putting together the 22 images obtained at the end of this calculation, from (i) to (f) and then from (f) to (i). It allows to visualize the MEP.

    Tip

    Open the timages_04o_HIST.nc file with agate or qAgate to produce this animation.

  1. tolimg

    Come back to nimage=12. First you can increase tolimg to 0.001 and recompute the MEP. This will be much faster than in the previous case.

    Then you should decrease tolimg to 0.00001 and recompute the MEP. To gain CPU time, you can start your calculation by using the 12 images obtained at the end of the calculation that used tolimg = 0.0001. In your input file, these starting images will be specified by the keywords xcart, xcart_2img, xcart_3imgxcart_12img. You can copy them directly from the output file obtained at the previous section. The graph below superimposes the path obtained with 12 images and tolimg=0.001 (grey curve) and the one with 12 images and tolimg=0.0001 (cyan curve).

    image

    Total energy as a function of OH distance for the path computed with 12 images and tolimg=0.0001 (cyan curve) and the one computed with 12 images and tolimg=0.001 (grey curve).