diff --git a/docs.it4i/software/chemistry/phono3py.md b/docs.it4i/software/chemistry/phono3py.md index 9277cbea77b5c2c7d9630ea0eeb28dcf859630d8..70d0e5120cd8d1ad8c9a7e4f8abb8605e54181fd 100644 --- a/docs.it4i/software/chemistry/phono3py.md +++ b/docs.it4i/software/chemistry/phono3py.md @@ -2,9 +2,9 @@ ## Introduction -This GPL software calculates phonon-phonon interactions via the third order force constants. It allows to obtain lattice thermal conductivity, phonon lifetime/linewidth, imaginary part of self energy at the lowest order, joint density of states (JDOS) and weighted-JDOS. For details see Phys. Rev. B 91, 094306 (2015) and [website][a]. +This GPL software calculates phonon-phonon interactions via the third order force constants. It allows obtaining lattice thermal conductivity, phonon lifetime/linewidth, imaginary part of self energy at the lowest order, joint density of states (JDOS), and weighted-JDOS. For details, see Phys. Rev. B 91, 094306 (2015) and [website][a]. -Available modules +Available modules: ```console $ ml av phono3py @@ -18,7 +18,7 @@ $ ml phono3py ### Calculating Force Constants -One needs to calculate second order and third order force constants using the diamond structure of silicon stored in [POSCAR][1] (the same form as in VASP) using single displacement calculations within supercell. +You need to calculate second order and third order force constants using the diamond structure of silicon stored in [POSCAR][1] (the same form as in VASP) using single displacement calculations within supercell. ```console $ cat POSCAR @@ -61,7 +61,7 @@ POSCAR-00006 POSCAR-00015 POSCAR-00024 POSCAR-00033 POSCAR-00042 POSCAR-00051 POSCAR-00007 POSCAR-00016 POSCAR-00025 POSCAR-00034 POSCAR-00043 POSCAR-00052 POSCAR-00061 POSCAR-00070 POSCAR-00079 POSCAR-00088 POSCAR-00097 POSCAR-00106 ``` -For each displacement the forces needs to be calculated, i.e. in form of the output file of VASP (vasprun.xml). For a single VASP calculations one needs [KPOINTS][2], [POTCAR][3], and [INCAR][4] in your case directory (where you have POSCARS) and those 111 displacements calculations can be generated by [prepare.sh][5] script. Then each of the single 111 calculations is submitted [run.sh][6] by [submit.sh][7]. +For each displacement, the forces needs to be calculated, i.e. in form of the output file of VASP (vasprun.xml). For a single VASP calculations, you need [KPOINTS][2], [POTCAR][3], and [INCAR][4] in your case directory (where you have POSCARS) and those 111 displacements calculations can be generated by the [prepare.sh][5] script. Then each of the single 111 calculations is submitted [run.sh][6] by [submit.sh][7]. ```console $./prepare.sh @@ -76,7 +76,7 @@ disp-00007 disp-00015 disp-00023 disp-00031 disp-00039 disp-00047 disp-00055 dis disp-00008 disp-00016 disp-00024 disp-00032 disp-00040 disp-00048 disp-00056 disp-00064 disp-00072 disp-00080 disp-00088 disp-00096 disp-00104 disp_fc3.yaml ``` -Taylor your run.sh script to fit into your project and other needs and submit all 111 calculations using submit.sh script +Tailor your run.sh script to fit into your project and other needs and submit all 111 calculations using the submit.sh script ```console $ ./submit.sh @@ -84,23 +84,23 @@ $ ./submit.sh ## Collecting Results and Post-Processing With Phono3py -Once all jobs are finished and vasprun.xml is created in each disp-XXXXX directory the collection is done by +Once all jobs are finished and vasprun.xml is created in each disp-XXXXX directory, the collection is done by: ```console $ phono3py --cf3 disp-{00001..00111}/vasprun.xml ``` -and `disp_fc2.yaml, FORCES_FC2`, `FORCES_FC3` and disp_fc3.yaml should appear and put into the HDF format by +and `disp_fc2.yaml, FORCES_FC2`, `FORCES_FC3` and disp_fc3.yaml should appear and put into the HDF format by: ```console $ phono3py --dim="2 2 2" -c POSCAR ``` -resulting in `fc2.hdf5` and `fc3.hdf5` +resulting in `fc2.hdf5` and `fc3.hdf5`. ### Thermal Conductivity -The phonon lifetime calculations takes some time, however is independent on grid points, so could be splitted: +The phonon lifetime calculations take some time; however, it is independent on grid points, so it can be split: ```console $ phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" --sigma 0.1 --wgp @@ -149,19 +149,19 @@ ir_grid_points: # [address, weight] * grid_point: 364 ``` -One finds which grid points needed to be calculated, for instance using following: +You can find which grid points needed to be calculated, for instance, using: ```console $ phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" -c POSCAR --sigma 0.1 --br --write-gamma --gp="0 1 2 ``` -One calculates grid points 0, 1, 2. To automize one can use for instance scripts to submit 5 points in series, see [gofree-cond1.sh[8].] +You can calculate grid points 0, 1, 2. To automate, use for instance, scripts to submit 5 points in series, see [gofree-cond1.sh[8].] ```console $ qsub gofree-cond1.sh ``` -Finally the thermal conductivity result is produced by grouping single conductivity per grid calculations using +Finally, the thermal conductivity result is produced by grouping single conductivity per grid calculations using ```console $ phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" --br --read_gamma