<div dir="ltr">Dear all, There is a problem regarding to the umbrella sampling I am using the CP2K 2.6 The following is my input file. I would like to add harmonic constraint to sample the free energy as a function of distance between geometry center of atoms 1270..1276 and a plane (can be defined from atoms 91..93). However, it always gives me segmentation fault... I have defined the collective variable (COLVAR) in &subsys section, and try to add constraint in &MOTION&CONSTRAINT&COLLECTIVE Any suggestions/help are warm welcomed. Thank you guys in advance! Best Regards, CZ FRONTIERS IN SIMULATION TECHNOLOGY C.J. Mundy, S. Balasubramanian, Ken Bagchi, J. Hutter, Ari Seitsonen IFW Kuo, T. Laino, J. VandeVondele Version 1.0 Program received signal SIGSEGV: Segmentation fault - invalid memory reference. Backtrace for this error: #0 0x1DB74DD in _gfortrani_show_backtrace at backtrace.c:260 #1 0x1D93CA6 in _gfortrani_backtrace_handler at compile_options.c:129 #2 0x40BAEF in _L_unlock_16 at bar.c:0 #3 0xBFA720 in __colvar_types_MOD_colvar_setup at colvar_types.F:1138 #4 0xBE6B2A in __colvar_methods_MOD_colvar_read at colvar_methods.F:1100 #5 0xC8588D in __cp_subsys_methods_MOD_cp_subsys_read_colvar at cp_subsys_methods.F:90 #6 0xD254CF in __fist_environment_MOD_fist_init at fist_environment.F:171 #7 0x46F042 in __fist_main_MOD_fist_create_force_env at fist_main.F:92 #8 0x68C7A3 in __qmmm_main_MOD_qmmm_create_force_env_low at qmmm_main.F:466 #9 0x68FA7B in __qmmm_main_MOD_qmmm_create_force_env at qmmm_main.F:178 #10 0x449AE9 in __f77_interface_MOD_create_force_env at f77_interface.F:854 #11 0x41304B in __cp2k_runs_MOD_cp2k_run at cp2k_runs.F:318 #12 0x416F6B in __cp2k_runs_MOD_run_input at cp2k_runs.F:1161 #13 0x40D7B7 in cp2k at cp2k.F:307 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! setting variables for short !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! @SET DIR /home/caoz/qmmm/test @SET VAR PhosphateOnPt !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! global variables to do the general control !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! &GLOBAL PRINT_LEVEL MEDIUM PREFERRED_FFT_LIBRARY FFTSG PROJECT ${VAR} RUN_TYPE MD &END GLOBAL !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! start from "restart" file !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !&EXT_RESTART ! RESTART_FILE_NAME ${DIR}/${VAR}.restart ! RESTART_DEFAULT .TRUE. ! ! RESTART_COUNTERS .FALSE. ! RESTART_AVERAGES .FALSE. !&END EXT_RESTART !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! propagate your system !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! &MOTION !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! the moving part !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! &MD ENSEMBLE NVT STEPS 1000000 TIMESTEP 0.1 TEMPERATURE 300.0 ! TEMP_TOL 50.0 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! thermostat for NVT !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! &THERMOSTAT TYPE NOSE REGION GLOBAL &NOSE TIMECON 1. &END NOSE &END THERMOSTAT !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! output general info. for your system !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! &PRINT &ENERGY FILENAME =${DIR}/${VAR}.ener &EACH MD 1 &END EACH &END ENERGY &PROGRAM_RUN_INFO &EACH MD 1 &END EACH &END PROGRAM_RUN_INFO &END PRINT &END MD &CONSTRAINT !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! these atoms will not move, but they contribute to force and energy !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! &FIXED_ATOMS LIST 1..120 &END FIXED_ATOMS !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! define umbrella spring constant !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! &COLLECTIVE COLVAR 2000 MOLECULE 1 TARGET 6.4 &RESTRAINT K .05 &END &END &END CONSTRAINT !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! output detailed dynamics of your system !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! &PRINT !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! coordinates !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! &TRAJECTORY FILENAME =${DIR}/${VAR}.xyz FORMAT XYZ &EACH MD 1 &END EACH &END TRAJECTORY !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! velocities !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! &VELOCITIES FILENAME =${DIR}/${VAR}.vel FORMAT XYZ &EACH MD 1 &END EACH &END VELOCITIES !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! forces !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! &FORCES FILENAME =${DIR}/${VAR}.for FORMAT XYZ &EACH MD 1 &END EACH &END FORCES !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! restart !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! &RESTART FILENAME =${DIR}/${VAR}.restart BACKUP_COPIES 1 &EACH MD 10 &END EACH &END RESTART &RESTART_HISTORY OFF &END RESTART_HISTORY &END PRINT &END MOTION !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! define how to calculate force !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! &FORCE_EVAL METHOD QMMM &MM &FORCEFIELD !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! empirical force field !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! PARM_FILE_NAME ${DIR}/par PARMTYPE CHM VDW_SCALE14 0.0000000000000000E+00 EI_SCALE14 0.0000000000000000E+00 &SPLINE RCUT_NB 0.7000000000000009E+01 EMAX_SPLINE 1.0000000000000000E+1000 &END SPLINE &NONBONDED &GENPOT ATOMS OT Pt RCUT 26.4562 RMIN 0.188973 RMAX 26.4562 VARIABLES R PARAMETERS A alpha VALUES 64.74957 11 FUNCTION A*(R**(-alpha)) &END GENPOT &GENPOT ATOMS OT Pt RCUT 26.4562 RMIN 0.188973 RMAX 26.4562 VARIABLES R PARAMETERS C VALUES 0.6474957 FUNCTION C*(R**(-6)) &END GENPOT &SIEPMANN ATOMS OT Pt B 0.6 BETA 10. D 0.54656 E 0.0156 F 13.3 RCUT 6.04712 &END SIEPMANN &END NONBONDED &END FORCEFIELD !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! electrostatic part !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! &POISSON &EWALD EWALD_TYPE spme ALPHA .5 GMAX 14 15 80 &END EWALD &END POISSON &END MM &DFT CHARGE -1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! pseudo-potential !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! BASIS_SET_FILE_NAME ${DIR}/GTH_BASIS_SETS POTENTIAL_FILE_NAME ${DIR}/GTH_POTENTIALS !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! wave function used for initial guess !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! WFN_RESTART_FILE_NAME ${DIR}/RESTART &MGRID CUTOFF 300 COMMENSURATE T &END MGRID !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! iteration methods and criteria !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! &SCF MAX_SCF 10 EPS_SCF 1.0E-5 SCF_GUESS RESTART &OUTER_SCF EPS_SCF 1.0E-5 MAX_SCF 1 &END !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! orbital transformation !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! &OT PRECONDITIONER FULL_ALL MINIMIZER CG STEPSIZE 0.15 &END OT &PRINT &RESTART FILENAME =${DIR}/RESTART &END RESTART &END PRINT &END SCF !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! Ab initio/Quickstep parameters !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! &QS METHOD GAPW EPS_GVG 1.0E-5 EPS_PGF_ORB 1.0E-5 EXTRAPOLATION ASPC EXTRAPOLATION_ORDER 3 PW_GRID NS-FULLSPACE PW_GRID_BLOCKED FREE &END QS !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! exchange !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! &XC &XC_GRID XC_SMOOTH_RHO NN50 XC_DERIV SPLINE2_SMOOTH &END XC_GRID &XC_FUNCTIONAL NO_SHORTCUT &PBE T PARAMETRIZATION PBESOL &END PBE &END XC_FUNCTIONAL &VDW_POTENTIAL POTENTIAL_TYPE PAIR_POTENTIAL &PAIR_POTENTIAL TYPE DFTD3 PARAMETER_FILE_NAME ${DIR}/dftd3.dat REFERENCE_FUNCTIONAL PBE &END PAIR_POTENTIAL &END VDW_POTENTIAL &END XC !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! electrostatic for QM part !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! &POISSON PERIODIC XYZ &EWALD ALPHA 0.5 GMAX 14 15 80 EWALD_TYPE SPME &END EWALD &END POISSON &END DFT !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! coupling between QM and MM !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! &QMMM E_COUPL GAUSS USE_GEEP_LIB 12 NOCOMPATIBILITY T &CELL ABC 13.8741420 14.4184314 80. PERIODIC xyz &END CELL !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! this is recommended to maintain the hydrogen bond... !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! &MM_KIND OT RADIUS 1.2000000000000000E+00 &END MM_KIND &MM_KIND HT RADIUS 4.0000000000000002E-01 &END MM_KIND !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! define your QM atoms !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! &QM_KIND Pt ! MM_INDEX 1..120 ! &END QM_KIND &QM_KIND P MM_INDEX 1270 &END QM_KIND &QM_KIND O MM_INDEX 1271 1272 1273 1274 &END QM_KIND &QM_KIND H MM_INDEX 1275 1276 &END QM_KIND !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! image charge method !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! &IMAGE_CHARGE DETERM_COEFF ITERATIVE EXT_POTENTIAL -1 IMAGE_RESTART_FILE_NAME ${DIR}/${VAR}.image MM_ATOM_LIST 91..120 &END IMAGE_CHARGE &END QMMM !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! define your system !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! &SUBSYS !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! PBC !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! &CELL ABC 13.8741420 14.4184314 80. PERIODIC xyz &END CELL !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! coordinates !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! &COORD @include 'coord.xyz' &END COORD !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! topology !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! &TOPOLOGY CONN_FILE_FORMAT PSF CONN_FILE_NAME ${DIR}/${VAR}.psf &END TOPOLOGY !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! define your collective variable !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! &COLVAR &DISTANCE_POINT_PLANE ATOM_POINT 2000 &POINT ATOMS 1270..1276 TYPE GEO_CENTER WEIGHTS 31./97. 16./97. 16./97. 16./97. 16./97. 1./97. 1./97. &END POINT ATOMS_PLANE 91 92 93 &END DISTANCE_POINT_PLANE &END !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! pseudo-potential !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! &KIND O BASIS_SET DZVP-GTH POTENTIAL GTH-PBE-q6 &END KIND &KIND H BASIS_SET DZVP-GTH POTENTIAL GTH-PBE-q1 &END KIND &KIND P BASIS_SET DZVP-GTH POTENTIAL GTH-PBE-q5 &END KIND &KIND Pt BASIS_SET DZVP-MOLOPT-SR-GTH POTENTIAL GTH-PBE-q10 &END KIND &END SUBSYS &PRINT &PROGRAM_RUN_INFO &EACH MD 1 &END EACH &END PROGRAM_RUN_INFO &END PRINT &END FORCE_EVAL </div>