Add missing workflow inputs and READMEs for full example

full_example_TiO2_2_100K/step1_MD/README.md

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+# Project_relaxation_recombination_TiO2_nanoclusters
+
+**inputs and scripts to be in the same directory to start the calculation**
+
+**inputs**:
+
+AIMD is performed with CP2K. The folder contains the relaxed (TiO2)2 geometry at 100 K as case
+example (`pos.xyz`), and cp2k input (`md.inp`) for performing the MD run.
+
+
+**scripts**:
+
+The `submit.slm` file for performing step 1 calculation in a HPC.
+
+**outputs**:
+
+3000 steps AIMD generated trajectory: `trajectory_TiO2_2_100K.xyz`
+
+-------------
+
+To prepare this step, combine all input and script files in the same folder and run:
+
+    sbatch submit.slm

full_example_TiO2_2_100K/step1_MD/inputs/md.inp

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+ &GLOBAL
+   PRINT_LEVEL  MEDIUM
+   PROJECT_NAME TiO2_02_08
+   RUN_TYPE  MD
+ &END GLOBAL
+ &FORCE_EVAL
+  METHOD  QS
+  &DFT
+    UKS .FALSE. 
+    BASIS_SET_FILE_NAME BASIS_MOLOPT
+    POTENTIAL_FILE_NAME POTENTIAL 
+    &MGRID
+      NGRIDS 12
+      CUTOFF 300
+      REL_CUTOFF 50
+    &END MGRID
+    &QS
+      METHOD GPW
+      EPS_DEFAULT 1.000E-14
+    &END QS
+    &POISSON
+      PSOLVER MT 
+      PERIODIC NONE
+    &END
+    &SCF
+      &DIAGONALIZATION ON
+      &END DIAGONALIZATION
+      &MIXING
+        ALPHA 0.3
+        METHOD BROYDEN_MIXING
+        NBROYDEN 8
+      &END MIXING
+      EPS_SCF 1.0E-6
+      SCF_GUESS ATOMIC
+      MAX_SCF  50
+      ADDED_MOS 50
+    &END SCF
+    &XC
+      &XC_FUNCTIONAL
+         &PBE
+         &END PBE
+      &END XC_FUNCTIONAL
+      &VDW_POTENTIAL
+         POTENTIAL_TYPE PAIR_POTENTIAL 
+         &PAIR_POTENTIAL
+            PARAMETER_FILE_NAME dftd3.dat
+            TYPE DFTD3
+            REFERENCE_FUNCTIONAL PBE
+            R_CUTOFF [angstrom] 16
+         &END
+      &END VDW_POTENTIAL
+    &END XC
+    &PRINT
+      &MULLIKEN OFF
+      &END
+      &HIRSHFELD OFF
+      &END
+    &END PRINT
+  &END DFT
+  &SUBSYS
+
+    &CELL
+      A         10.000000000         0.0000000000         0.0000000000
+      B         0.0000000000        10.000000000         0.0000000000
+      C         0.0000000000         0.0000000000         10.000000000
+      PERIODIC  NONE 
+    &END CELL
+    &VELOCITY
+	6.11464E-05	-5.08645E-05	5.9453E-05
+        0.000164537	2.67605E-05	-8.76053E-05
+        -0.000173724	-0.000100692	0.000115461
+        2.1818E-05	8.05143E-05	-4.80069E-05
+        -0.000170792	-0.00010392	1.85E-05
+        -6.87189E-05	8.89652E-05	-8.06625E-05
+    &END VELOCITY
+
+    &TOPOLOGY
+      COORD_FILE_NAME pos.xyz
+      COORD_FILE_FORMAT XYZ
+      ! These two lines to center the geometry in the cell
+      &CENTER_COORDINATES T
+      &END
+    &END
+
+    &KIND  Ti
+      BASIS_SET DZVP-MOLOPT-SR-GTH 
+      POTENTIAL GTH-PBE-q12 
+    &END KIND
+    &KIND  O
+      BASIS_SET DZVP-MOLOPT-GTH
+      POTENTIAL GTH-PBE-q6
+    &END KIND
+  &END SUBSYS
+ &END FORCE_EVAL
+
+&MOTION
+ &MD
+   ENSEMBLE NVT
+   TEMPERATURE [K] 100   #make it larger 3200
+   TIMESTEP [fs] 1.0
+   STEPS 4000
+   &THERMOSTAT
+     REGION GLOBAL
+     TYPE NOSE
+	 &NOSE
+           ! adapt it based on the Ti-O stretch mode frequency
+	   TIMECON 100
+	 &END
+   &END THERMOSTAT
+ &END
+ &PRINT
+   &TRAJECTORY
+     &EACH
+       MD 1
+     &END EACH
+   &END TRAJECTORY
+   &VELOCITIES ON
+   &END VELOCITIES
+   &FORCES ON
+   &END FORCES
+   &RESTART
+     BACKUP_COPIES 1
+     &EACH
+       MD 1
+     &END EACH
+   &END RESTART
+ &END PRINT 
+&END 

full_example_TiO2_2_100K/step1_MD/inputs/pos.xyz

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+6
+
+Ti 6.234433 4.992303 4.509986
+O 7.477660 4.994919 5.560046
+O 4.961883 6.329328 4.982885
+Ti 3.787933 4.999196 5.482860
+O 2.470030 5.016240 4.494639
+O 5.023272 3.684964 4.983873

full_example_TiO2_2_100K/step1_MD/inputs/submit_1.slm

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+#!/bin/bash -l
+#SBATCH --account=alexeyak
+##SBATCH --partition=valhalla  --qos=valhalla
+##SBATCH --clusters=faculty
+#SBATCH --partition=general-compute  --qos=general-compute
+#SBATCH --clusters=ub-hpc
+##SBATCH --partition=scavenger  --qos=scavenger
+#SBATCH --time=72:00:00
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=12
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=64000
+###SBATCH -C CPU-Gold-6130 
+###SBATCH --mail-user=mshakiba@buffalo.edu
+echo "SLURM_JOBID="$SLURM_JOBID
+echo "SLURM_JOB_NODELIST="$SLURM_JOB_NODELIST
+echo "SLURM_NNODES="$SLURM_NNODES
+echo "SLURMTMPDIR="$SLURMTMPDIR
+echo "working directory="$SLURM_SUBMIT_DIR
+
+# Here load whatever which is needed for running CP2K
+# Load VMD if cube visualization flag is turned on
+load vmd
+module use /projects/academic/cyberwksp21/MODULES
+module load cp2k/v24/avx512
+module load libra/devel # load the devel version for alignment
+
+# For slurm environments
+export I_MPI_PMI_LIBRARY=/usr/lib64/libpmi.so
+export OMP_NUM_THREADS=1
+
+
+mpirun -np 9 cp2k.psmp -i md.inp -o out-md-2x2.log
+
+

full_example_TiO2_2_100K/step2_TDDFT_Excitations/README.md

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+# Project_relaxation_recombination_TiO2_nanoclusters
+
+**inputs and scripts to be in the same directory to start the calculation**
+
+**inputs**:
+
+Aligned AIMD trajectory for this (TiO2)2 system at 100 Ke (`dynamcis_AIMD-aligned_100K.xyz`).
+
+CP2K input where TD-DFT options are detailed (`es_diag_temp.inp`).
+
+**scripts**:
+
+`distribute_jobs.py` is the file that you need modify by specifying initial and final step of the trajectory and the number of jobs. Libra will split the trajectory based on these values and will submit them by creating the specific folders for each job.
+
+`run_template.py`: A file that contains the data to run the MO overlap calculations. It is important to properly define the Active Space. In this case we have chosen orbitals going from 24-15 to 25+15. 24th and 25th orbitals are respectively the HOMO and the LUMO.
+
+The `submit_template.slm` file is the one which will be submitted and runs the python `run.py` where the `run.py` file is the copy of the `run_template.py` file but with the initial and final steps filled based on the requested number of jobs and the initial and final step for the trajectory.
+
+`vmd_input_template`: The VMD input template. This input will be modified by Libra but only the mol load cube and rendering line, render Tachyon ... will be changed. You can make your own input template by opening the VMD on your computer and from File choose Log Tcl commands to file... and it will append all the commands for reproducing that image into a file.
+
+To start the TD-DFT calculation simply run: **python distribute_jobs.py**
+
+
+
+**outputs**:
+
+All logfiles with TD-DFT CP2K output information are included in `logfiles_TiO2_2_100K.tar.bz2`.
+`res_TiO2_2_100K.tar.bz2`contains all KS energies (E_ks_*); MO overalps (S_ks_*) and time-overlaps (St_ks_*).
+
+To unpack, decompress each file separately:
+
+    tar -xvjf logfiles_TiO2_2_100K.tar.bz2
+    tar -xvjf res_TiO2_2_100K.tar.bz2
+
+

full_example_TiO2_2_100K/step2_TDDFT_Excitations/inputs/distribute_jobs.py

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+import os
+import sys
+import libra_py.packages.cp2k.methods as CP2K_methods
+
+
+run_slurm = True
+submit_template = 'submit_template.slm'
+run_python_file = 'run_template.py'
+istep = 1000
+fstep = 4000 
+njobs = 10 
+submission_exe = 'sbatch'
+# Removing the previous folders if existed. You can keep them as well 
+# but Libra will overwrite some of the data if their names are the same
+os.system('rm -rf res job* all_*')
+
+print('Distributing jobs...')
+CP2K_methods.distribute_cp2k_libint_jobs(submit_template, run_python_file, istep, fstep, njobs, run_slurm, submission_exe)
+