added some minimal examples

NEB/examples/water_flip_g16_excited_state/neb.gjf

@@ -0,0 +1,13 @@
+%Chk=grad.chk
+%Nproc=1
+%Mem=1Gb
+# B3LYP/def2SVP Force td(nstates=2, root=1)
+NoSymm 
+
+s1 gradient
+
+0 1
+@geom
+
+
+

NEB/examples/water_flip_g16_excited_state/neb_main_g16.sub

@@ -0,0 +1,25 @@
+#!/bin/bash
+# for Slurm
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=1
+#SBATCH --mem=1Gb
+#SBATCH --job-name=neb_main_g16
+#SBATCH --output=neb_main_g16.err
+
+xyz=water_flip.xyz
+SCRATCHDIR=/sscratch/${SLURM_JOBID}
+
+cd $SLURM_SUBMIT_DIR
+
+optimize_neb $xyz \
+             --procs_per_image=4 \
+             --mem_per_image=1Gb \
+             --parallel_images=10 \
+             --scratch_dir=$SCRATCHDIR \
+             --print_every=1 \
+             --integrator=bfgs \
+             --optimize_endpoints \
+             --calculator=g16 \
+          &> neb_main_g16.out
+
+echo "FINISHED"

NEB/examples/water_flip_g16_excited_state/water_flip.xyz

@@ -0,0 +1,50 @@
+3
+File written by XYZ.py
+   h 0.811165000000000 0.834945000000000 0.000000000000000
+   o 0.177670000000000 0.000000000000000 0.000000000000000
+   h 0.811165000000000 -0.834945000000000 0.000000000000000
+3
+File written by XYZ.py
+   h 0.630906111111111 0.834945000000000 0.000000000000000
+   o 0.138187777777778 0.000000000000000 0.000000000000000
+   h 0.630906111111111 -0.834945000000000 0.000000000000000
+3
+File written by XYZ.py
+   h 0.450647222222222 0.834945000000000 0.000000000000000
+   o 0.098705555555556 0.000000000000000 0.000000000000000
+   h 0.450647222222222 -0.834945000000000 0.000000000000000
+3
+File written by XYZ.py
+   h 0.270388333333333 0.834945000000000 0.000000000000000
+   o 0.059223333333333 0.000000000000000 0.000000000000000
+   h 0.270388333333333 -0.834945000000000 0.000000000000000
+3
+File written by XYZ.py
+   h 0.090129444444444 0.834945000000000 0.000000000000000
+   o 0.019741111111111 0.000000000000000 0.000000000000000
+   h 0.090129444444444 -0.834945000000000 0.000000000000000
+3
+File written by XYZ.py
+   h -0.090129444444444 0.834945000000000 0.000000000000000
+   o -0.019741111111111 0.000000000000000 0.000000000000000
+   h -0.090129444444444 -0.834945000000000 0.000000000000000
+3
+File written by XYZ.py
+   h -0.270388333333333 0.834945000000000 0.000000000000000
+   o -0.059223333333333 0.000000000000000 0.000000000000000
+   h -0.270388333333333 -0.834945000000000 0.000000000000000
+3
+File written by XYZ.py
+   h -0.450647222222222 0.834945000000000 0.000000000000000
+   o -0.098705555555555 0.000000000000000 0.000000000000000
+   h -0.450647222222222 -0.834945000000000 0.000000000000000
+3
+File written by XYZ.py
+   h -0.630906111111111 0.834945000000000 0.000000000000000
+   o -0.138187777777778 0.000000000000000 0.000000000000000
+   h -0.630906111111111 -0.834945000000000 0.000000000000000
+3
+File written by XYZ.py
+   h -0.811165000000000 0.834945000000000 0.000000000000000
+   o -0.177670000000000 0.000000000000000 0.000000000000000
+   h -0.811165000000000 -0.834945000000000 0.000000000000000

NEB/examples/water_flip_qchem/neb_main_qchem.sub

@@ -0,0 +1,25 @@
+#!/bin/bash
+# for Slurm
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=1
+#SBATCH --mem=1Gb
+#SBATCH --job-name=neb_main_g16
+#SBATCH --output=neb_main_g16.err
+
+xyz=water_flip.xyz
+SCRATCHDIR=/sscratch/${SLURM_JOBID}
+
+cd $SLURM_SUBMIT_DIR
+
+optimize_neb $xyz \
+             --procs_per_image=4 \
+             --mem_per_image=1Gb \
+             --parallel_images=10 \
+             --scratch_dir=$SCRATCHDIR \
+             --print_every=1 \
+             --integrator=bfgs \
+             --optimize_endpoints \
+             --calculator=qchem \
+          &> neb_main_g16.out
+
+echo "FINISHED"

NEB/examples/water_flip_qchem/water_flip.xyz

@@ -0,0 +1,50 @@
+3
+File written by XYZ.py
+   h 0.811165000000000 0.834945000000000 0.000000000000000
+   o 0.177670000000000 0.000000000000000 0.000000000000000
+   h 0.811165000000000 -0.834945000000000 0.000000000000000
+3
+File written by XYZ.py
+   h 0.630906111111111 0.834945000000000 0.000000000000000
+   o 0.138187777777778 0.000000000000000 0.000000000000000
+   h 0.630906111111111 -0.834945000000000 0.000000000000000
+3
+File written by XYZ.py
+   h 0.450647222222222 0.834945000000000 0.000000000000000
+   o 0.098705555555556 0.000000000000000 0.000000000000000
+   h 0.450647222222222 -0.834945000000000 0.000000000000000
+3
+File written by XYZ.py
+   h 0.270388333333333 0.834945000000000 0.000000000000000
+   o 0.059223333333333 0.000000000000000 0.000000000000000
+   h 0.270388333333333 -0.834945000000000 0.000000000000000
+3
+File written by XYZ.py
+   h 0.090129444444444 0.834945000000000 0.000000000000000
+   o 0.019741111111111 0.000000000000000 0.000000000000000
+   h 0.090129444444444 -0.834945000000000 0.000000000000000
+3
+File written by XYZ.py
+   h -0.090129444444444 0.834945000000000 0.000000000000000
+   o -0.019741111111111 0.000000000000000 0.000000000000000
+   h -0.090129444444444 -0.834945000000000 0.000000000000000
+3
+File written by XYZ.py
+   h -0.270388333333333 0.834945000000000 0.000000000000000
+   o -0.059223333333333 0.000000000000000 0.000000000000000
+   h -0.270388333333333 -0.834945000000000 0.000000000000000
+3
+File written by XYZ.py
+   h -0.450647222222222 0.834945000000000 0.000000000000000
+   o -0.098705555555555 0.000000000000000 0.000000000000000
+   h -0.450647222222222 -0.834945000000000 0.000000000000000
+3
+File written by XYZ.py
+   h -0.630906111111111 0.834945000000000 0.000000000000000
+   o -0.138187777777778 0.000000000000000 0.000000000000000
+   h -0.630906111111111 -0.834945000000000 0.000000000000000
+3
+File written by XYZ.py
+   h -0.811165000000000 0.834945000000000 0.000000000000000
+   o -0.177670000000000 0.000000000000000 0.000000000000000
+   h -0.811165000000000 -0.834945000000000 0.000000000000000

README.md

@@ -68,13 +68,13 @@ using the nudged elastic band (NEB) algorithm.
 #### Initial Path
 The initial path for the NEB should be interpolated between the two minimum structures. There are two different 
 algorithms that can be used. Either a linear interpolation (in internal coordinates), which is a for example a part
-of the DFTBaby package by A. Humeniuk (see interpolate_linearly.py in DFTBaby). The more sophisticated way is to use 
+of the DFTBaby package by A. Humeniuk (see `interpolate_linearly.py` in DFTBaby). The more sophisticated way is to use 
 the geodesic interpolation algorithm developed by T. Martinez and coworkers (see [Ref.](https://aip.scitation.org/doi/full/10.1063/1.5090303)).
 Their algorithm is implemented in a python package and can be obtained from their [Github repository](https://github.com/virtualzx-nad/geodesic-interpolate).
 A number of 12 to 16 interpolated structures is often a good choice. 
 
 
-###Interface to Gaussian 16 or 09
+#### Interface to Gaussian 16 or 09
 In addition you have to set up a Gaussian input script called `neb.gjf`
  that computes the gradient and saves it in a checkpoint file called
  'grad.chk'. The geometry is updated via a file called `geom` that
@@ -97,7 +97,7 @@ In addition you have to set up a Gaussian input script called `neb.gjf`
   --------------------------------------
  ```
 
-###Interface to Q-Chem 
+#### Interface to Q-Chem 
 To use the NEB package in combination with Q-Chem you have to prepare a Q-Chem input
 script called `neb.in`. Within this input file it is important that you request a force calculation
 and that a Checkpoint file will be written. An example input script is shown below:
@@ -139,7 +139,7 @@ $rem
 ```
 
 
-### Visualization of results
+#### Visualization of results
 After successful minimization of the reaction pathn you can plot the energy of the path during each iteration. Within the 
 directory where the `neb_####.xyz` and `path_energies_####.dat` files are located, you can just call:
 ```
@@ -151,8 +151,15 @@ This will open a Matplotlib window where you can slide through the iterations as
 
 ### Examples
 
-A minimal example with a submit script can be found in the NEB/examples directory. Make sure that the optimize_neb script
-is within your PATH variable, so that it can be called from the command-line. 
+Some examples with a submit script can be found in the NEB/examples directory.
+- `water_flip_g16`: Reaction path of water flip with Gaussian16 in the singlet ground state at the DFT level.
+- `water_flip_g16_excited_state`: Reaction path of water flip with Gaussian16 in the first singlet excited state at the DFT level.
+- `water_flip_qchem`: Reaction path of water flip with Q-Chem in the singlet ground state at the DFT level.<br>
+<br>
+Make sure that the `optimize_neb` script
+is within your `PATH variable, so that it can be called from the command-line. The NEB computations can be performed in the
+  electronic ground state as well as in the excited state. The interfaces allow these features at least for Gaussian 16 and Q-Chem. Optimization
+  within the frame of spin-polarised/unrestricted wave functions are also possible and tested with Gaussian 16 and Q-Chem. 
 
 --------------
 Optional arguments: