目录

Dimer method to calculate saddle point

H diffusion in a frozen Ir lattice

Input files

atom.config 

     5
 LATTICE
      3.84347853     0.00000000     0.00000000
      0.00000000     3.84347853     0.00000000
      0.00000000     0.00000000     3.84347853
 POSITION
  77     0.12500000     0.12500000     0.12500000 0 0 0
  77     0.12500937     0.63473653     0.63473930 1 1 1
  77     0.63473766     0.12500788     0.63474031 1 1 1
  77     0.63473926     0.63473848     0.12501068 1 1 1
   1     0.47985749     0.47985229     0.47985339 1 1 1
 DIMER_DIR_N
  77         0.000000000000000         0.000000000000000         0.000000000000000 #element number, fractional coordinates of direction
  77        -0.012059410733252        -0.012827111941020        -0.008025300664088
  77        -0.013847872075022        -0.009967273033432        -0.007927057981427
  77        -0.013434331335085        -0.012626295573776        -0.003144488942515
   1         0.071022910801012         0.074799719412651         0.085081889050619

DIMER_DIR_N: specifies the initial direction along the dimer.

etot.input 

 1  4
 JOB = DIMER
 IN.ATOM = atom.config
 IN.PSP1 = Ir.SG15.PBE.UPF
 IN.PSP2 = H.SG15.PBE.UPF
 ECUT = 50
 ECUT2 = 200
 MP_N123 = 5 5 5 0 0 0 3
 E_ERROR = 0.0
 FERMIDE = 0.2

JOB = DIMER: specifies a calculation of dimer method.

Ir.SG15.PBE.UPF, H.SG15.PBE.UPF

Calculations

  1. You can submit PWmat tasks in different ways:
   mpirun -np 4 PWmat | tee output

Run the command directly 

   #!/bin/bash
   #PBS -N SCF
   #PBS -l nodes=1:ppn=4
   #PBS -q batch
   #PBS -l walltime=100:00:00
 
   ulimit -s unlimited
   cd $PBS_O_WORKDIR
 
   mpirun -np 4 PWmat | tee output

Submit the task with a pbs script

  1. For DIMER calculation, the final configuration is writen in final.config, the configurations of each translation step ore in MOVEMENT.

Another file DIMERSTEPS can be used to check the convergency, dates in DIMERSTEPS: 

STEP         FORCE      FORCE/dR        ENERGY     CURVATURE         ANGLE        NSTEPS      DISTANCE
        MAX(eV/Ang) ROT(eV/Ang^2)          (eV)                         ROT           ROT         TRANS
    1       0.97540       3.24074  -11578.64674      -0.04126       0.04787             1       0.10000
    2       0.33231       1.08127  -11578.67713      -0.03043       0.03043             1      -0.07131
    3       0.40229       1.16503  -11578.67639      -0.02366       0.01931             1       0.02685
    4       0.19611       0.94741  -11578.68556      -0.02616       0.01533             1       0.10000
    5       0.19684       0.70913  -11578.68577      -0.02493       0.01250             1      -0.00189
    6       0.21610       1.98167  -11578.68433      -0.02524       0.02234             1       0.10000
    7       0.15590       1.31524  -11578.68344      -0.02669       0.01483             1       0.03999
    8       0.27853       1.01864  -11578.68047      -0.02487       0.01141             1       0.04234
    9       0.07919       0.72661  -11578.68151      -0.02434       0.01165             1       0.02893
    10       0.07897       0.88689  -11578.68147      -0.02679       0.01048             1       0.00062
    11       0.08531       0.57502  -11578.68097      -0.02615       0.00763             1       0.01706
    12       0.02929       1.68360  -11578.68063      -0.02664       0.02057             1       0.03746 *
  1. STEP: the index of current transition step.
  2. FORCE MAX: the maximum of current transition step, unit $$eV/\text{\AA}$$.
  3. FORCE ROT/dR: the rotational force / dimer_dR, unit $$eV/\text{\AA}^2$$.
  4. ENERGY: the energy of the dimer center, unit eV.
  5. CURVATURE: the curvature along the dimer.
  6. ANGLE ROT: the number of rotated in rotational steps, unit rad.
  7. NSTEPS ROT: the number of rotational steps in current transiton step.
  8. DISTANCE TRANS: the step size of current transition step, unit Bohr.