diff --git a/docs.it4i/software/chemistry/phono3py.md b/docs.it4i/software/chemistry/phono3py.md index 70d0e5120cd8d1ad8c9a7e4f8abb8605e54181fd..12b0cb816db9ac466a08f34654e247e44a3be633 100644 --- a/docs.it4i/software/chemistry/phono3py.md +++ b/docs.it4i/software/chemistry/phono3py.md @@ -47,7 +47,7 @@ $ phono3py -d --dim="2 2 2" -c POSCAR ``` 111 displacements is created stored in -disp_fc3.yaml, and the structure input files with this displacements are POSCAR-00XXX, where the XXX=111. +`disp_fc3.yaml`, and the structure input files with this displacements are `POSCAR-00XXX`, where the `XXX=111`. ```console disp_fc3.yaml POSCAR-00008 POSCAR-00017 POSCAR-00026 POSCAR-00035 POSCAR-00044 POSCAR-00053 POSCAR-00062 POSCAR-00071 POSCAR-00080 POSCAR-00089 POSCAR-00098 POSCAR-00107 @@ -90,7 +90,7 @@ Once all jobs are finished and vasprun.xml is created in each disp-XXXXX directo $ 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 @@ -155,13 +155,13 @@ You can find which grid points needed to be calculated, for instance, using: $ phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" -c POSCAR --sigma 0.1 --br --write-gamma --gp="0 1 2 ``` -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].] +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