CP/MM Tutorial

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sub < Some batch script templates called launch_XXX.job can be found in: /home/ei250498/TUTORIALS/ACETONE If you open them you will found some initial lines starting with #BSUB word that represents commands for the batch system: #BSUB -J Template #BSUB -o output #BSUB -e error #BSUB -n 2 #BSUB -W 00:15 #BSUB -M 700 #BSUB -a intelmpi ß Batch system’s job name ß Filename of the batch system’s output messages (and error if no option -e used) ß Filename of the batch system’s error messages ß Number of cores to be reserve for the job ß Hard runtime limit: after the expiration of this time (here 15’) the job will be killed ß Set the per-process memory limit in MB ß Specify which MPI version you want to use in the parallel run followed by some lines which are the commands that the batch system has to run on the computational nodes and that are similar to the ones you use in the interactive way. Refer to the HPC user guide for a more detailed description of all the useful commands available for the batch script. To check the status of your batched jobs you can use the command: bjobs –w and to remove a job from the batch list you can use the command: bkill where the job_id can be read from the list got with the bjobs command. A batch script template called launch.job can be found in: /home/ei250498/TUTORIALS/ACETONE Refer to the HPC user guide to learn how to create a batch script for your jobs. To run CPMD with for example 2 cores (everything on the same line): mpirun –np 2 cpmd.x /home/ei250498/PROGRAMS/SRC/cpmd/PP > & /home/ei250498/PROGRAMS/SRC/cpmd/PP is the location where CPMD will look for the pseudopotentials files which will be specified in the input file. All the pseudopotentials we will use are already present there. In order to calculate the dipole moment of the acetone in vacuum we first have to optimize the geometry of the molecule we have constructed in the previous step. So,
we need to write an appropriate input file according the syntax of CPMD. 3 By your favorite editor, write down the opt_geo.inp text file: &INFO Acetone molecule Geometry optimization &END &CPMD OPTIMIZE GEOMETRY XYZ CONVERGENCE ORBITALS 1.0d-7 CONVERGENCE GEOMETRY 7.0d-4 &END &SYSTEM ANGSTROM SYMMETRY ORTHORHOMBIC CELL ABSOLUTE 10.6 10.0 9.8 0.0 0.0 0.0 CUTOFF 70. &END &DFT FUNCTIONAL BLYP &END &ATOMS *C_MT_BLYP.psp KLEINMAN-BYLANDER LMAX=D 3 0.000000 0.000000 0.000000 1.367073 0.000000 -0.483333 -0.683537 -1.183920 -0.483333 *O_MT_BLYP.psp KLEINMAN-BYLANDER LMAX=D 1 0.000000 0.000000 1.220000 *H_MT_BLYP.psp KLEINMAN-BYLANDER LMAX=P 6 1.367073 0.000000 -1.572333 1.880433 0.889165 -0.120333 1.880433 -0.889165 -0.120333 -0.683537 -1.183920 -1.572333 -0.170177 -2.073085 -0.120333 -1.710256 -1.183920 -0.120333 &END CPMD Input file 3 CPMD manual: http://www.cpmd.org/manual.pdf
Page 1 and 2: CP/MM Tutorial Jülich, 26/07/2012
Page 3: Then, you can run molden by simply
Page 7 and 8: The first line gives the number of
Page 9 and 10: NR TYPE X(bohr) Y(bohr) Z(bohr) MBL
Page 11 and 12: NUMBER OF PLANE WAVES FOR WAVEFUNCT
Page 13 and 14: average force on the atoms, and the
Page 15 and 16: RESTART.1 Restart binary file from
Page 17 and 18: g09 opt_geom.com & 3. After about o
Page 19 and 20: edit ACET You can also check if all
Page 21 and 22: Box Density • mkdir analysis •
Page 23 and 24: %FLAG SCEE_SCALE_FACTOR and %FLAG S
Page 25 and 26: simulation is similar to the CPMD i
Page 27 and 28: the according dimension per line. T
Page 29 and 30: TEMPERATURE: EMASS: TIMESTEP: MAXST
Page 31 and 32: MM_CELL_TRANS ENERGIES The QM syste
Page 33 and 34: NOSE ENERGY IONS 0.000000 0.00000 C
Page 35 and 36: cd HEATING • Copy the following f
Page 37 and 38: meaningful. Therefore, we must alwa
Page 39 and 40: mpirun -np 2 cpmd.x dipole.inp /hom

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