Feature: tools for selective dynamics with ABACUS + Phonopy

tools/README.md

@@ -1,14 +1,25 @@
 SIAB: codes to generate numerical atomic orbitals.
+
 molden: generate molden style file for Multiwfn analysis. 
 
 plot-tools: band structure, dos and pdos, dipole and adsorption.
+
 rt-tddft-tools: tools for real-time tddft.
+
 average_pot: python script used to calculate and plot the average electrostatic potential.
+
 stm: generate figures related to Scanning tunneling microscope technique.
 
 generate_orbital.sh: script used to generate numerical atomic orbitals (NAO).
+
 opt_abfs_bash: related to generating NAO basis set.
+
 opt_lcao_bash: related to generating NAO basis set.
+
 opt_orb_pytorch: related to generating NAO basis set.
+
 opt_orb_pytorch_dpsi: related to generating NAO basis set.
+
 qo: generate quasiatomic orbital (qo).
+
+selective_dynamics: used to do selective dynamics with ABACUS + Phonopy.

tools/selective_dynamics/README.md

@@ -0,0 +1,105 @@
+# Selective Dynamics for ABACUS+Phonopy
+
+## Requirements
+
+- [ase-abacus](https://gitlab.com/1041176461/ase-abacus)
+- [Phonopy](https://github.com/phonopy/phonopy)
+
+## Usage
+
+### Setting
+
+There is a setting file named `config.yaml`:
+```yaml
+origin_structure: 'STRU'     # the original structure
+selected_indices: [18, 19]   # the atom index that you concerned about, start from 0
+tasks_per_batch: 12          # how much jobs per batch
+wait_time: 600               # s, sleep time between batches
+
+setting_conf: |
+  SYMMETRY = .FALSE. 
+  DIM = 1 1 1 
+  DISPLACEMENT_DISTANCE = 0.03
+
+mesh.conf: |
+  DIM = 1 1 1
+  MESH = 31 31 31
+  TMAX = 2000
+  TSTEP = 2
+
+input: |
+  INPUT_PARAMETERS
+  #Parameters (1.General)
+  suffix                 phonon
+  calculation            scf
+  symmetry               1
+  nspin                  1
+  pseudo_dir             /fs2/home/chenkg/2_liuyu/3_abacus/PP_ORB/pseudo
+  orbital_dir            /fs2/home/chenkg/2_liuyu/3_abacus/PP_ORB/efficiency
+  kpoint_file            ../KPT
+
+  #Parameters (2.Iteration)
+  ecutwfc                100
+  scf_thr                1e-8
+  scf_nmax               100
+
+  #Parameters (3.Basis)
+  basis_type             lcao
+  ks_solver              genelpa
+  gamma_only             0
+
+  #Parameters (4.Smearing)
+  smearing_method        gaussian
+  smearing_sigma         0.001
+
+  #Parameters (5.Mixing)
+  mixing_type            broyden
+  mixing_beta            0.7
+
+  cal_force              1
+  cal_stress             1
+
+kpt: |
+  K_POINTS
+  0
+  Gamma
+  5 5 1 0 0 0
+
+job_script: |
+  #!/bin/bash
+  #SBATCH -p cp6
+  #SBATCH -N 1
+  #SBATCH -J abacus
+  #SBATCH -n 28
+
+  source /fs2/home/chenkg/2_liuyu/3_abacus/abacus_env.sh
+  export OMP_NUM_THREADS=28
+
+  mpirun -n 1 abacus
+```
+
+- origin_structure: The `STRU` filename, which contains both the fixed atoms and the free atoms.
+- selected_indices: The indexs of the free atoms. Note that the index starts from 0.
+- tasks_per_batch: How much jobs submitted per batch.
+- wait_time: Sleep time between batches, the unit is second.
+- setting_conf: The `setting.conf` file for Phonopy.
+- mesh.conf: The `mesh.conf` file for Phonopy.
+- input: The `INPUT` file for ABACUS.
+- kpt: The `KPT` file for ABACUS.
+- job_script: The script used to submit jobs.
+
+### Submit jobs
+
+Use the following command
+```bash
+python3 path_to_selective_dynamics.py --submit
+```
+to generate displaced structures and submit jobs.
+
+### Postprocess
+
+Use the following command
+```bash
+python3 path_to_selective_dynamics.py --post
+```
+to generate `FORCE_SETS` and results of phonon calculations.

tools/selective_dynamics/example/FORCE_SETS

@@ -0,0 +1,62 @@
+2    
+12   
+
+1    
+  0.0149999999999997  -0.0259807621135333   0.0000000000000000
+   0.0237018506   -0.0443837983    4.6170588819
+  -0.0237018506    0.0443837983   -4.6170588819
+
+1    
+ -0.0149999999999997   0.0259807621135333   0.0000000000000000
+  -0.0265865716    0.0427183038    4.6170588819
+   0.0265865716   -0.0427183038   -4.6170588819
+
+1    
+  0.0149999999999997   0.0259807621135333   0.0000000000000000
+   0.0265865717    0.0427183036    4.6170588822
+  -0.0265865717   -0.0427183036   -4.6170588822
+
+1    
+ -0.0149999999999997  -0.0259807621135333   0.0000000000000000
+  -0.0237018502   -0.0443837983    4.6170588821
+   0.0237018502    0.0443837983   -4.6170588821
+
+1    
+  0.0000000000000000   0.0000000000000000   0.0300000000000000
+   0.0000000000    0.0000000000    3.2278781929
+   0.0000000000    0.0000000000   -3.2278781929
+
+1    
+  0.0000000000000000   0.0000000000000000  -0.0300000000000000
+   0.0000000000    0.0000000000    5.8048931631
+   0.0000000000    0.0000000000   -5.8048931631
+
+2    
+  0.0149999999999997  -0.0259807621135333   0.0000000000000000
+  -0.0161713742    0.0279335705    4.6172988628
+   0.0161713742   -0.0279335705   -4.6172988628
+
+2    
+ -0.0149999999999997   0.0259807621135333   0.0000000000000000
+   0.0161054946   -0.0279716061    4.6172988630
+  -0.0161054946    0.0279716061   -4.6172988629
+
+2    
+  0.0149999999999997   0.0259807621135333   0.0000000000000000
+  -0.0161054946   -0.0279716062    4.6172988628
+   0.0161054946    0.0279716062   -4.6172988628
+
+2    
+ -0.0149999999999997  -0.0259807621135333   0.0000000000000000
+   0.0161713742    0.0279335705    4.6172988628
+  -0.0161713742   -0.0279335705   -4.6172988627
+
+2    
+  0.0000000000000000   0.0000000000000000   0.0300000000000000
+   0.0000000000    0.0000000000    5.8781504371
+   0.0000000000    0.0000000000   -5.8781504371
+
+2    
+  0.0000000000000000   0.0000000000000000  -0.0300000000000000
+   0.0000000000    0.0000000000    3.1693579055
+   0.0000000000    0.0000000000   -3.1693579055

tools/selective_dynamics/example/STRU

@@ -0,0 +1,46 @@
+ATOMIC_SPECIES
+C  12.01  C.upf
+O  16  O.upf
+
+NUMERICAL_ORBITAL
+C_gga_8au_100Ry_2s2p1d.orb
+O_gga_6au_100Ry_2s2p1d.orb
+
+LATTICE_CONSTANT
+1.889727000000
+
+LATTICE_VECTORS
+3.700890000000  -6.410129513223  0.000000000000
+3.700890000000  6.410129513223  0.000000000000
+0.000000000000  0.000000000000  15.000000000000
+
+ATOMIC_POSITIONS
+Direct
+
+C
+0
+19
+0.111111111111  0.222222222222  0.500000000000  
+0.111111111111  0.555555555556  0.500000000000  
+0.111111111111  0.888888888889  0.500000000000  
+0.444444444444  0.222222222222  0.500000000000  
+0.444444444444  0.555555555556  0.500000000000  
+0.444444444444  0.888888888889  0.500000000000  
+0.777777777778  0.222222222222  0.500000000000  
+0.777777777778  0.555555555556  0.500000000000  
+0.777777777778  0.888888888889  0.500000000000  
+0.222222222222  0.111111111111  0.500000000000  
+0.222222222222  0.444444444444  0.500000000000  
+0.222222222222  0.777777777778  0.500000000000  
+0.555555555556  0.111111111111  0.500000000000  
+0.555555555556  0.444444444444  0.500000000000  
+0.555555555556  0.777777777778  0.500000000000  
+0.888888888889  0.111111111111  0.500000000000  
+0.888888888889  0.444444444444  0.500000000000  
+0.888888888889  0.777777777778  0.500000000000  
+0.888888888889  0.777777777778  0.620000000000  
+
+O
+0
+1
+0.888888888889  0.777777777778  0.698000000000  

tools/selective_dynamics/example/config.yaml

@@ -0,0 +1,65 @@
+origin_structure: 'STRU'     # the original structure
+selected_indices: [18, 19]   # the atom index that you concerned about, start from 0
+tasks_per_batch: 12          # how much jobs per batch
+wait_time: 600               # s, sleep time between batches
+
+setting.conf: |
+  SYMMETRY = .FALSE. 
+  DIM = 1 1 1 
+  DISPLACEMENT_DISTANCE = 0.03
+
+mesh.conf: |
+  DIM = 1 1 1
+  MESH = 31 31 31
+  TMAX = 2000
+  TSTEP = 2
+
+input: |
+  INPUT_PARAMETERS
+  #Parameters (1.General)
+  suffix                 phonon
+  calculation            scf
+  symmetry               1
+  nspin                  1
+  pseudo_dir             /fs2/home/chenkg/2_liuyu/3_abacus/PP_ORB/pseudo
+  orbital_dir            /fs2/home/chenkg/2_liuyu/3_abacus/PP_ORB/efficiency
+  kpoint_file            ../KPT
+
+  #Parameters (2.Iteration)
+  ecutwfc                100
+  scf_thr                1e-8
+  scf_nmax               100
+
+  #Parameters (3.Basis)
+  basis_type             lcao
+  ks_solver              genelpa
+  gamma_only             0
+
+  #Parameters (4.Smearing)
+  smearing_method        gaussian
+  smearing_sigma         0.001
+
+  #Parameters (5.Mixing)
+  mixing_type            broyden
+  mixing_beta            0.7
+
+  cal_force              1
+  cal_stress             1
+
+kpt: |
+  K_POINTS
+  0
+  Gamma
+  5 5 1 0 0 0
+
+job_script: |
+  #!/bin/bash
+  #SBATCH -p cp6
+  #SBATCH -N 1
+  #SBATCH -J abacus
+  #SBATCH -n 28
+
+  source /fs2/home/chenkg/2_liuyu/3_abacus/abacus_env.sh
+  export OMP_NUM_THREADS=28
+
+  mpirun -n 1 abacus