1 Installation

1.1 Download

Download SSAdNDP from http://ion.chem.usu.edu/~boldyrev/ssadndp.php

1.2 Install New Periodic NBO

1.2.1 New Periodic NBO (2015)

Ref: http://bbs.keinsci.com/thread-12111-1-1.html

tar -xvf  periodic_nbo_v.1.1.tgz
cd  projection
sed -i "s/USE mkl95_BLAS/USE BLAS95/ig;s/USE mkl95_LAPACK/USE LAPACK95/ig" *.f90
sed -i "s/zGEMM_MKL95/GEMM/ig;s/DGEMM_MKL95/GEMM/ig;" *.f90
sed -i "s/DGETRF_MKL95/GETRF/ig;s/ZGETRF_MKL95/GETRF/ig;" *.f90
sed -i "s/DGETRI_MKL95/GETRI/ig;s/ZGETRI_MKL95/GETRI/ig;" *.f90
sed -i "s/zheev_mkl95/heev/ig;s/ZGESVD_MKL95/GESVD/ig;s/ZGEMV_MKL95/GEMV/ig;" *.f90
###Modify Makefile
LD=ifort
FC=ifort
FFLAGS= -I$(MKLROOT)/include/intel64/lp64 -mkl=sequential
LDFLAGS=-L$(MKLROOT)/lib/intel64 -openmp -lmkl_blas95_lp64 -lmkl_lapack95_lp64 -lpthread -lm -I$(MKLROOT)/include/intel64/lp64 -mkl=sequential
###
make 

##Periodic nbo 
tar -xvf periodic_nbo_v.1.1.tgz
cd  projection
sed -i "s/USE mkl95_BLAS/USE BLAS95/ig;s/USE mkl95_LAPACK/USE LAPACK95/ig" *.f90
sed -i "s/zGEMM_MKL95/GEMM/ig;s/DGEMM_MKL95/GEMM/ig;" *.f90
sed -i "s/DGETRF_MKL95/GETRF/ig;s/ZGETRF_MKL95/GETRF/ig;" *.f90
sed -i "s/DGETRI_MKL95/GETRI/ig;s/ZGETRI_MKL95/GETRI/ig;" *.f90
sed -i "s/zheev_mkl95/heev/ig;s/ZGESVD_MKL95/GESVD/ig;s/ZGEMV_MKL95/GEMV/ig;" *.f90

###Modify Makefile.template
FC=ifort
LD=ifort
#FFLAGS=-check all -check noarg_temp_created -g -traceback -warn unused -I $(MKLROOT)/include/intel64/lp64
FFLAGS= -vec-report0 -openmp -I $(MKLROOT)/include/intel64/lp64
LDFLAGS=-L$(MKLROOT)/lib/intel64 -lmkl_core -lmkl_intel_lp64 -lmkl_sequential -lmkl_blas95_lp64 -lmkl_lapack95_lp64 -openmp
###
make

1.3 NBO version vasp

cp projection_output.F proj_VASP_5.4_mod.patch /src
cd src && patch<proj_VASP_5.4_mod.patch
# ps: proj_VASP_5.4_mod.patch modifiled from proj_VASP_5.4.patch in Per NBO  
make std   
mv bin/vasp_std  bin/vasp.impi.nbo
mv build/std build/std.nbo

1.4 install SSAdNDP (old Periodic NBO)

tar -xvf  projection_v.1.1.2.tgz && cd projection  
make (not use)    
tar -xvf  SSAdNDP_program_distr.zip && cd SSAdNDP_program_distr  
cd SSAdNDP/
#------------------
change the PATH for MKL  in Makefile.template, then
#------------------
perl mkmf -t Makefile.template -p ssadndp.exe  
make && cp ssadndp.exe ~/.soft/vasp/vaspshell/  
cd ../Visualization
ifort -o visual.exe  visual.f90 
cp visual.exe  ~/.soft/vasp/vaspshell/  
cd Projection
#---------------
correct MKLROOT, 
#---------------
make
cp projection ~/.soft/vasp/vaspshell/projection.exe
 get projection,  use this one rather the one in projection_v.1.1.2.tgz

2 Example

Add LNBO=.FALSE.; LWAVE=.TRUE. to INCAR of single point calculation and run mpirun -np 16 vasp.impi.nbo.
Modify INCAR file, add LNBO=.TRUE.; ISTART=1; EDIFF=1E-5 and delete NPAR (important) and run mpirun -np 16 vasp.impi.nbo again. Tip: The parallel calculation of VASP is based on bands, so “NBANDS” will be times of cores used. But too many unoccupied bands will lead to unphysical eigenvalue, leading to failure of projection at the next step. So do not use too many cores.
At bash shell, runexport OMP_NUM_THREADS=4 && export OMP_STACKSIZE=4000mb && ulimit -s unlimited.
Prapare basis.inp file from ${soft_root}/gaussian/basis/6-311G.g94, basis.inp like

****
B     0
S   6   1.00
   2858.8900000              0.00215375
    428.1400000              0.0165823
     97.5282000              0.0821870
     27.9693000              0.2766180
      8.2157700              0.6293160
      1.1127800              0.1737700
SP   3   1.00
     13.2415000              0.1174430              0.0418100
      3.0016600              0.9180020              0.2365750
      0.9128560             -0.00265105             0.8162140
SP   1   1.00
      0.3154540              1.0000000              1.0000000
SP   1   1.00
      0.0988563              1.0000000              1.0000000
D   1   1.00
      0.4010000              1.0000000
****
C     0
S   6   1.00
   4563.2400000              0.00196665
    682.0240000              0.0152306
    154.9730000              0.0761269
     44.4553000              0.2608010
     13.0290000              0.6164620
      1.8277300              0.2210060
SP   3   1.00
     20.9642000              0.1146600              0.0402487
      4.8033100              0.9199990              0.2375940
      1.4593300             -0.00303068             0.8158540
SP   1   1.00
      0.4834560              1.0000000              1.0000000
SP   1   1.00
      0.1455850              1.0000000              1.0000000
D   1   1.00
      0.6260000              1.0000000
****

and run projection.exe at bash shell.
5. Convert CONTCAR to vasp 4 format (no element line). Prepare SSAdNDP.inp like this

GENERAL SEARCH INPUT FILE
Prepare files for visualization: T/F?
T
Number of different types of bonds in general search:
4
Number of centers, ON threshold, Distance threshold:
1 1.85 2.0
2 1.75 2.0
3 1.85 2.5
4 1.75 3.0

and run ssadndp.exe SSAdNDP.inp resid_gen.dat T.
6. You should delete resid_gen.dat for a new scheme, while you should keep it for continuing searching. For user directed mode, Prepare SSAdNDP-UD.inp like this

USER-DIRECTED SEARCH INPUT FILE
Prepare files for visualization: T/F?
T
Number of fragments to search on:
2
Number of centers on fragment 1:
7
Atom numbers, cell a,b,c:
2, 0 0 0
4, 0 0 0
5, 0 0 0
13, 0 0 0
8, 0 0 0
10,0 0 0
12,0 0 0
Number of bonds on fragment 1:
1
Number of centers on fragment 2:
7
Atom numbers, cell a,b,c:
1, 0 0 0
3, 0 0 0
6, -1 -1 0
7, 0 -1 0
9, 0 -1 0
11, 0 0 0
14, -1 0 0
Number of bonds on fragment 2:
1

and run ssadndp.exe SSAdNDP-UD.inp resid_gen.dat T. Tips: Translating the fragment may avoid the belt on the edge.
7. If you get vis_gs_*-bonds.out from general mode or vis_ud_bonds.out from user directed mode, run visual.exe vis_gs_4c-bonds.out 81 81 81 T or run visual.exe vis_ud_bonds.out 81 81 81 T.
8. Open lattice_vec.cube in VESTA, uncheck Style->Volumetric data->Show Sections.
9. in Vesta, Edit->Edit Data->Phases, import cube file (e.g., gs_3c-bond_1.cube or ud_bond_1.cube), and set positioning for this layer to “0.5 0.5 0.5” ( or 0.16666/0.83333 rather than 0.5) and Apply.