[CP2K-user] Automated Topology Builder (ATB) force fields and CP2K

ar...@gmail.com ar26... at gmail.com
Thu Dec 24 12:42:10 UTC 2020


Dear all,

I want to do a CP2K simulation of Chloroform using classical force fields. 
The force fields are generated with Automated Topology Builder (ATB). It 
gives you the force field parameters in a file called "54a7.ifp" in 
Gromos96 format (which I included in the &FORCEFIELD section), the topology 
file "chl_g96.top" and the structure "chl.g96" (which I included in the 
&TOPOLOGY section). However the program fails with the below output (input 
files are also attached). Does anyone have any idea why is the program 
failing? Also, if I want to simulate N Chloroform molecules instead of only 
one, do I need to explicitly write the topology of each molecule or is 
there a way to say that I have N molecules of the given topology?

Best regards,

Alejandro.



 DBCSR| Multiplication driver                                               
XSMM
 DBCSR| Multrec recursion 
limit                                              512
 DBCSR| Multiplication stack size                                           
1000
 DBCSR| Maximum elements for images                                    
UNLIMITED
 DBCSR| Multiplicative factor virtual 
images                                   1
 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                                              0


  **** **** ******  **  PROGRAM STARTED AT               2020-12-24 
13:19:55.324
 ***** ** ***  *** **   PROGRAM STARTED ON                             
fullerene
 **    ****   ******    PROGRAM STARTED BY                                 
ar612
 ***** **    ** ** **   PROGRAM PROCESS ID                                 
20488
  **** **  *******  **  PROGRAM STARTED IN 
/cluster/data/ar612/fullerene/cp2k/eq
                                           uilibration/mm/chl_test

 CP2K| version string:                                          CP2K 
version 6.1
 CP2K| source code revision number:                                    
svn:18464
 CP2K| cp2kflags: omp libint fftw3 libxc elpa=201705 elpa_qr parallel mpi3 
scala
 CP2K|            pack xsmm libderiv_max_am1=6 libint_max_am=7 plumed2 mkl
 CP2K| is freely available from                            
https://www.cp2k.org/
 CP2K| Program compiled at                         Sun Mar 29 16:22:44 CEST 
2020
 CP2K| Program compiled on                                             
fullerene
 CP2K| Program compiled for                     
intel_mkl_blas_init_xsmm_xc_elpa
 CP2K| Data directory path       
/data/ar612/programs/intel/2017/cp2k/6.1.0/data
 CP2K| Input file name                                              
chl_test.inp
 
 GLOBAL| Force Environment 
number                                              1
 GLOBAL| Basis set file name                                           
BASIS_SET
 GLOBAL| Potential file name                                           
POTENTIAL
 GLOBAL| MM Potential file name                                     
MM_POTENTIAL
 GLOBAL| Coordinate file name                                            
chl.g96
 GLOBAL| Method name                                                        
CP2K
 GLOBAL| Project name                                                   
chl_test
 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| Total number of message passing 
processes                             1
 GLOBAL| Number of threads for this 
process                                   24
 GLOBAL| This output is from 
process                                           0
 GLOBAL| CPU model name :  Intel(R) Xeon(R) CPU           E5645  @ 2.40GHz

 MEMORY| system memory details [Kb]
 MEMORY|                        rank 0           min           max       
average
 MEMORY| MemTotal             49551460      49551460      49551460      
49551460
 MEMORY| MemFree               7285744       7285744       7285744       
7285744
 MEMORY| Buffers               4978552       4978552       4978552       
4978552
 MEMORY| Cached               34197572      34197572      34197572      
34197572
 MEMORY| Slab                  2446576       2446576       2446576       
2446576
 MEMORY| SReclaimable          2401476       2401476       2401476       
2401476
 MEMORY| MemLikelyFree        48863344      48863344      48863344      
48863344



                      ************* ******** ***********   
                     ************* **********************  
                     ****     **** ****      ***********   
                     ******** ****  *******     ****       
                     *******  ****   *******   ****        
                     ****     ****       ****  ****        
                     ****     **** **********  ****        
                      ****     **** ********    ****       
                     FRONTIERS IN SIMULATION TECHNOLOGY    
                                                           
                        C.J. Mundy, S. Balasubramanian,    
                     Ken Bagchi, J. Hutter, Ari Seitsonen  
                      IFW Kuo, T. Laino, J. VandeVondele   
                                 Version 1.0               

                                                           


 EWALD| Summation is done by:                                               
SPME
 EWALD| Alpha parameter [       ANGSTROM^-1]                              
0.4000
 EWALD| Real Space Cutoff [          ANGSTROM]                            
8.4348
 EWALD| G-space max. Miller index                         54        
54        54
 EWALD| Spline interpolation 
order                                             4
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC                Routine            Line        
Source             
cp2k.ssmp          000000000A869D01  Unknown               Unknown  Unknown
cp2k.ssmp          000000000A867E3B  Unknown               Unknown  Unknown
cp2k.ssmp          000000000A735374  Unknown               Unknown  Unknown
cp2k.ssmp          000000000A735186  Unknown               Unknown  Unknown
cp2k.ssmp          000000000A6C1F39  Unknown               Unknown  Unknown
cp2k.ssmp          000000000A6CB326  Unknown               Unknown  Unknown
libpthread-2.12.s  0000003C2DA0F7E0  Unknown               Unknown  Unknown
cp2k.ssmp          000000000116BF09  topology_gromos_m         564  
topology_gromos.F
cp2k.ssmp          0000000000EEE783  topology_mp_conne         478  
topology.F
cp2k.ssmp          0000000000EEDB45  topology_mp_topol         186  
topology.F
cp2k.ssmp          0000000000C43747  cp_subsys_methods         158  
cp_subsys_methods.F
cp2k.ssmp          0000000000C65CD8  fist_environment_         166  
fist_environment.F
cp2k.ssmp          00000000015CBAB5  fist_main_mp_fist          96  
fist_main.F
cp2k.ssmp          0000000000B4B70F  f77_interface_mp_         770  
f77_interface.F
cp2k.ssmp          0000000000496F1C  cp2k_runs_mp_run_         271  
cp2k_runs.F
cp2k.ssmp          0000000000482813  MAIN__                    281  cp2k.F
cp2k.ssmp          000000000048149E  Unknown               Unknown  Unknown
libc-2.12.so       0000003C2D61ED1D  __libc_start_main     Unknown  Unknown
cp2k.ssmp          0000000000481329  Unknown               Unknown  Unknown








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