[CP2K-user] first principle MD in zeolite

Peiyao Wu wupeiy... at gmail.com
Wed Jul 17 14:31:03 UTC 2019


 

I'm running on a supercomputer in a research institute. I also added a line 
"LSD .TRUE." because it had an error of odd number of electrons. 

The out put is this:


 DBCSR| CPU Multiplication driver                                           
BLAS

 DBCSR| Multrec recursion limit                                            
  512

 DBCSR| Multiplication stack size                                           
1000

 DBCSR| Maximum elements for images                                    
UNLIMITED

 DBCSR| Multiplicative factor virtual images                               
    1

 DBCSR| Use multiplication densification                                   
    T

 DBCSR| Multiplication size stacks                                         
    3

 DBCSR| Number of 3D layers                                               
SINGLE

 DBCSR| Use MPI memory allocation                                          
    T

 DBCSR| Use RMA algorithm                                                  
    F

 DBCSR| Use Communication thread                                           
    T

 DBCSR| Communication thread load                                           
  87



  **** **** ******  **  PROGRAM STARTED AT               2019-07-17 
09:18:47.903

 ***** ** ***  *** **   PROGRAM STARTED ON                                
ln0006

 **    ****   ******    PROGRAM STARTED BY                                 
  pwu

 ***** **    ** ** **   PROGRAM PROCESS ID                                  
3398

  **** **  *******  **  PROGRAM STARTED IN 
/panfs/roc/groups/12/siepmann/pwu/tes

                                           t-cp2k/BCR-10-4-NPT


 CP2K| version string:                    CP2K version 7.0 (Development 
Version)

 CP2K| source code revision number:                                  
git:a55c4e4

 CP2K| cp2kflags: fftw3 parallel mpi3 scalapack                            
     

 CP2K| is freely available from                            
https://www.cp2k.org/

 CP2K| Program compiled at                          Fri Jul 12 17:38:01 CDT 
2019

 CP2K| Program compiled on                                                
ln0004

 CP2K| Program compiled for                                   
Linux-x86-64-intel

 CP2K| Data directory path           
/panfs/roc/groups/12/siepmann/pwu/cp2k/data

 CP2K| Input file name                                                    
md.inp

 

 GLOBAL| Force Environment number                                          
    1

 GLOBAL| Basis set file name            
/home/siepmann/pwu/cp2k/data/BASIS_MOLOP

 GLOBAL| Potential file name            
/home/siepmann/pwu/cp2k/data/GTH_POTENTI

 GLOBAL| MM Potential file name                                     
MM_POTENTIAL

 GLOBAL| Coordinate file name                                      
__STD_INPUT__

 GLOBAL| Method name                                                        
CP2K

 GLOBAL| Project name                                                      
  MOF

 GLOBAL| Preferred FFT library                                             
FFTW3

 GLOBAL| Preferred diagonalization lib.                                     
  SL

 GLOBAL| Run type                                                           
  MD

 GLOBAL| All-to-all communication in single precision                      
    F

 GLOBAL| FFTs using library dependent lengths                              
    F

 GLOBAL| Global print level                                                
  LOW

 GLOBAL| MPI I/O enabled                                                   
    T

 GLOBAL| Total number of message passing processes                         
    1

 GLOBAL| Number of threads for this process                                
    1

 GLOBAL| This output is from process                                       
    0

 GLOBAL| CPU model name                Intel(R) Xeon(R) CPU E5-2680 v3 @ 
2.50GHz


 MEMORY| system memory details [Kb]

 MEMORY|                        rank 0           min           max       
average

 MEMORY| MemTotal             65670968      65670968      65670968      
65670968

 MEMORY| MemFree               4173760       4173760       4173760       
4173760

 MEMORY| Buffers                  4220          4220          4220          
4220

 MEMORY| Cached               56787252      56787252      56787252      
56787252

 MEMORY| Slab                  1140136       1140136       1140136       
1140136

 MEMORY| SReclaimable           893684        893684        893684        
893684

 MEMORY| MemLikelyFree        61858916      61858916      61858916      
61858916


 

 GENERATE|  Preliminary Number of Bonds generated:                         
    0

 GENERATE|  Achieved consistency in connectivity generation.


 
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 **                                                ... make the atoms dance   
**

 **                                                                         
  **

 **            Copyright (C) by CP2K developers group (2000 - 2019)         
  **

 **                                                                         
  **

 
*******************************************************************************



 TOTAL NUMBERS AND MAXIMUM NUMBERS


  Total number of            - Atomic kinds:                               
    5

                             - Atoms:                                      
  686

                             - Shell sets:                                 
  686

                             - Shells:                                      
3467

                             - Primitive Cartesian functions:               
3276

                             - Cartesian basis functions:                   
9641

                             - Spherical basis functions:                   
8955


  Maximum angular momentum of- Orbital basis functions:                    
    2

                             - Local part of the GTH pseudopotential:      
    2

                             - Non-local part of the GTH pseudopotential:  
    3



 SCF PARAMETERS         Density guess:                                    
ATOMIC

                        
--------------------------------------------------------

                        max_scf:                                            
  20

                        max_scf_history:                                   
    0

                        max_diis:                                          
    4

                        
--------------------------------------------------------

                        eps_scf:                                        
1.00E-06

                        eps_scf_history:                                
0.00E+00

                        eps_diis:                                       
1.00E-01

                        eps_eigval:                                     
1.00E-05

                        
--------------------------------------------------------

                        level_shift [a.u.]:                                 
0.00

                        
--------------------------------------------------------

                        Outer loop SCF in use 

                        No variables optimised in outer loop

                        eps_scf                                         
1.00E-06

                        max_scf                                             
  10

                        No outer loop optimization

                        step_size                                       
5.00E-01

 

 MD| Molecular Dynamics Protocol 

 MD| Ensemble Type                                                         
  NVT

 MD| Number of Time Steps                                                  
  100

 MD| Time Step [fs]                                                         
0.50

 MD| Temperature [K]                                                       
77.00

 MD| Temperature tolerance [K]                                              
0.00

 MD| Print MD information every                                        1 
step(s)

 MD| File type     Print frequency[steps]                             File 
names

 MD| Coordinates            1                                      
MOF-pos-1.xyz

 MD| Velocities             1                                      
MOF-vel-1.xyz

 MD| Energies               1                                         
MOF-1.ener

 MD| Dump                   1                                      
MOF-1.restart

 

 ROT| Rotational Analysis Info 

 ROT| Principal axes and moments of inertia in atomic units:

 ROT|                                1                 2                 3

 ROT| EIGENVALUES            0.865428622E+10   0.875228727E+10   
0.934185610E+10

 ROT|      X                     0.811895120       0.355981637       
0.462713073

 ROT|      Y                    -0.583698550       0.479959905       
0.654930907

 ROT|      Z                     0.011059654      -0.801820157       
0.597463070

 ROT| Number of Rotovibrational vectors:     6


 Calculation of degrees of freedom

                                                      Number of atoms:     
  686

                                 Number of Intramolecular constraints:     
    0

                                 Number of Intermolecular constraints:     
    0

                                  Invariants(translation + rotations):     
    0

                                                   Degrees of freedom:      
2058



 Restraints Information

                                  Number of Intramolecular restraints:     
    0

                                  Number of Intermolecular restraints:     
    0


 THERMOSTAT| Thermostat Info for PARTICLES

 THERMOSTAT| Type of thermostat                               
Nose-Hoover-Chains

 THERMOSTAT| Nose-Hoover-Chain length                                      
    3

 THERMOSTAT| Nose-Hoover-Chain time constant [  fs]                        
33.36

 THERMOSTAT| Order of Yoshida integrator                                   
    3

 THERMOSTAT| Number of multiple time steps                                 
    2

 THERMOSTAT| Initial Potential Energy                                   
0.000000

 THERMOSTAT| Initial Kinetic Energy                                     
0.250916

 THERMOSTAT| End of Thermostat Info for PARTICLES


 ************************** Velocities initialization 
**************************

 Initial Temperature                                                     77.00 
K

 COM velocity:           -0.000000000000     -0.000000000000     
-0.000000000000

 
*******************************************************************************



 Spin 1


 Number of electrons:                                                       
1868

 Number of occupied orbitals:                                               
1868

 Number of molecular orbitals:                                              
1868


 Spin 2


 Number of electrons:                                                       
1867

 Number of occupied orbitals:                                               
1867

 Number of molecular orbitals:                                              
1867


 Number of orbital functions:                                               
8955

 Number of independent orbital functions:                                   
8955


 Extrapolation method: initial_guess



 SCF WAVEFUNCTION OPTIMIZATION


  ----------------------------------- OT 
---------------------------------------

  Minimizer      : DIIS                : direct inversion

                                         in the iterative subspace

                                         using   7 DIIS vectors

                                         safer DIIS on

  Preconditioner : FULL_KINETIC        : inversion of T + eS

  Precond_solver : DEFAULT

  stepsize       :    0.15000000                  energy_gap     :    
0.20000000

  eps_taylor     :   0.10000E-15                  max_taylor     :         
    4

  ----------------------------------- OT 
---------------------------------------


  Step     Update method      Time    Convergence         Total energy    
Change

  
------------------------------------------------------------------------------

Killed



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