Not being able to compile vtst tools with vaspcode

Vasp transition state theory tools

Moderator: moderators

Post Reply
KalpajyotiDihingia
Posts: 4
Joined: Mon May 24, 2021 7:22 am

Not being able to compile vtst tools with vaspcode

Post by KalpajyotiDihingia »

Dear Professor
I'm a beginner of vasp. I have downloaded vtsttools and scripts. I have understood about copying neb.F, dynmat.F, dimer.F, lanczos.F, sd.F, cg.F, qm.F, lbfgs.F, bfgs.F, fire.F, and opt.F from vasptool to vasp source directory, and to backup the old chain.F and replaced by chain.F file from vtsttool.

But I've not understood the last point to edit the makefile. It says to add "bfgs.o dynmat.o instanton.o lbfgs.o sd.o cg.o dimer.o bbm.o \
fire.o lanczos.o neb.o qm.o opt.o" in makefile in the variable source which defines which objects will be built, and add the following objects before chain.o:

I'm not able to find the term chain.o.
can you please explain where this line "bfgs.o dynmat.o instanton.o lbfgs.o sd.o cg.o dimer.o bbm.o fire.o lanczos.o neb.o qm.o opt.o" to be added in the makefile.

And also please explain me how to give path to the vtstscript

Can you please help me in this problem.

Thank you!
From Kalpa Dihingia
graeme
Site Admin
Posts: 1999
Joined: Tue Apr 26, 2005 4:25 am
Contact:

Re: Not being able to compile vtst tools with vaspcode

Post by graeme »

Hi Kalpa,

The list of object files is now located in src/.objects ; this is the file to modify.

To add the vtstscripts into your path, you would use a command such as:

export PATH=$PATH:/path_to/vtstscripts

where path_to is the path in which the vtstscripts directory is located. You would typically put this path modification into a startup file such as .profile or .bashrc so that it will be automatically set whenever you log in.
KalpajyotiDihingia
Posts: 4
Joined: Mon May 24, 2021 7:22 am

Re: Not being able to compile vtst tools with vaspcode

Post by KalpajyotiDihingia »

Hello Professor !
Thank you so much for your response,
I have added these in the /src/.object file before chain.o
$(VTST_OBJS) \
bfgs.o \
dynmat.o \
instanton.o \
lbfgs.o \
sd.o \
cg.o \
dimer.o \
bbm.o \
fire.o \
lanczos.o \
neb.o \
qm.o \
opt.o \
Copied all the files from vtstcode6.1/ to src/ directory of vasp, and replaced the lines in main.F mentioned in the installation guide. After that I entered "make veryclean in vasp root directory which cleans all the files from build directory"

After doing all these I gave command "make DEPS=1 -j4 all"

I found no errors... but at the end of the run it is showing this
------------------------------------------------------------------------------------------------------------------------------------------
o auger.o dmatrix.o phonon.o wannier_mats.o elphon.o core_con_mat.o embed.o extpot.o fftmpiw.o fftmpi_map.o fftw3d.o fft3dlib.o /usr/local/lib/libfftw3.a main.o -Llib -ldmy -Lparser -lparser -L/usr/lib/x86_64-linux-gnu -lscalapack-openmpi -L/usr/lib/x86_64-linux-gnu -llapack -L/usr/lib/x86_64-linux-gnu -lblas -L/usr/include/fftw3/lib/x86_64-linux-gnu -lfftw3 -lstdc++
make[2]: Leaving directory '/usr/local/vasp/vasp6.2.0/vasp.6.2.0/build/gam'
make[1]: Leaving directory '/usr/local/vasp/vasp6.2.0/vasp.6.2.0/build/gam'
----------------------------------------------------------------------------------------------------------------------------------------------------------

I'm not sure it has worked or not. I'm attaching the log file of the run. Can you please confirm me that it has compiled into the vasp and will be working for my desired calculations. Please inform me if there is any mistake during compilation of vasp. It will be very helpfull for me.

Moreover I've successfully added vtstscript to the path as you told and its working now.

Thank you !
From Kalpa Dihingia
Attachments
log.gz
(17.31 KiB) Downloaded 662 times
graeme
Site Admin
Posts: 1999
Joined: Tue Apr 26, 2005 4:25 am
Contact:

Re: Not being able to compile vtst tools with vaspcode

Post by graeme »

That looks good. You can try a test run and grep the OUTCAR for VTST.
KalpajyotiDihingia
Posts: 4
Joined: Mon May 24, 2021 7:22 am

Re: Not being able to compile vtst tools with vaspcode

Post by KalpajyotiDihingia »

Thank you sir for your kind response
The calculation is running when I used inputs for neb. But I m not able to visualize the reaction coordinates. How can I visualize. Can you please give me an Idea.
Thank you again
graeme
Site Admin
Posts: 1999
Joined: Tue Apr 26, 2005 4:25 am
Contact:

Re: Not being able to compile vtst tools with vaspcode

Post by graeme »

I use the nebmove.pl script. If you append a 0, it will make a movie of the initial path (POSCAR files) if you append a 1 it will make a movie of the final path (CONTCAR files). Then, a viewer such as ase-gui or xyz in our tsase package can play this file as a movie. But there is nothing special about these viewers or the movie file, which is just a concatenated set of POSCAR-style structure files along the NEB calculation.
KalpajyotiDihingia
Posts: 4
Joined: Mon May 24, 2021 7:22 am

Re: Not being able to compile vtst tools with vaspcode

Post by KalpajyotiDihingia »

Thank you so much Dr Graeme for your kind help and response
Post Reply