PROGRAM CPMD STARTED AT: Wed Jan 5 18:47:51 2005 ****** ****** **** **** ****** ******* ******* ********** ******* *** ** *** ** **** ** ** *** ** ** *** ** ** ** ** ** ** ******* ** ** ** ** *** ****** ** ** ** *** ******* ** ** ** ******* ****** ** ** ** ****** VERSION 3.9.2 COPYRIGHT IBM RESEARCH DIVISION MPI FESTKOERPERFORSCHUNG STUTTGART The CPMD consortium WWW: http://www.cpmd.org Mailinglist: cpmd-list@cpmd.org E-mail: cpmd@cpmd.org *** Jan 5 2005 -- 12:51:29 *** THE INPUT FILE IS: 4-gly-md-nvt.inp THIS JOB RUNS ON: opt13 THE CURRENT DIRECTORY IS: /tmp_mnt/rubberbandman/akohlmey/webpage/myhome/cpmd-tutor/reference/04-gly THE TEMPORARY DIRECTORY IS: /tmp_mnt/rubberbandman/akohlmey/webpage/myhome/cpmd-tutor/reference/04-gly THE PROCESS ID IS: 23569 THE JOB WAS SUBMITTED BY: akohlmey ****************************************************************************** * INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO * ****************************************************************************** * MD production of a glycine in gas phase. * * Using Nose-Hoover Thermostat Chains. * ****************************************************************************** CAR-PARRINELLO MOLECULAR DYNAMICS PATH TO THE RESTART FILES: ./ RESTART WITH OLD ORBITALS RESTART WITH OLD ION POSITIONS RESTART WITH OLD VELOCITIES ITERATIVE ORTHOGONALIZATION MAXIT: 30 EPS: 1.00E-06 MAXIMUM NUMBER OF STEPS: 500 STEPS PRINT INTERMEDIATE RESULTS EVERY 10001 STEPS STORE INTERMEDIATE RESULTS EVERY 10001 STEPS STORE INTERMEDIATE RESULTS EVERY 501 SELF-CONSISTENT STEPS NUMBER OF DISTINCT RESTART FILES: 1 TEMPERATURE IS CALCULATED ASSUMING EXTENDED BULK BEHAVIOR FICTITIOUS ELECTRON MASS: 400.0000 TIME STEP FOR ELECTRONS: 4.0000 TIME STEP FOR IONS: 4.0000 TRAJECTORIES ARE SAVED ON FILE EVERY 10 STEPS TRAJEC.xyz IS SAVED ON FILE EVERY 10 STEPS ELECTRON DYNAMICS: TEMPERATURE CONTROL (NOSE-HOOVER THERMOSTATS) TARGET KINETIK ENERGY(A.U.): 1.000000E-03 CHARACTERISTIC FREQUENCY(CM**-1): 10000.00 ION DYNAMICS: TEMPERATURE CONTROL (NOSE-HOOVER THERMOSTATS) TARGET TEMPERATURE(KELVIN): 3.000000E+02 CHARACTERISTIC FREQUENCY(CM**-1): 4000.00 NOSE PARAMETERS NUMBER OF THERMOSTATS (IONS) : 3 NUMBER OF THERMOSTATS (ELECTRONS) : 3 NUMBER OF THERMOSTATS (CELL) : 3 SCALING FOR ELEC. DOF : 6.00 NUMBER OF YOSHIDA-SUZUKI STEPS : 7 NUMBER OF INTEGRATION CYCLES (NIT): 1 SPLINE INTERPOLATION IN G-SPACE FOR PSEUDOPOTENTIAL FUNCTIONS NUMBER OF SPLINE POINTS: 2000 EXCHANGE CORRELATION FUNCTIONALS LDA EXCHANGE: SLATER (ALPHA = 0.66667) LDA CORRELATION: LEE, YANG & PARR [C.L. LEE, W. YANG, AND R.G. PARR, PRB 37 785 (1988)] GRADIENT CORRECTED FUNCTIONAL DENSITY THRESHOLD: 5.00000E-06 EXCHANGE ENERGY [A.D. BECKE, PHYS. REV. A 38, 3098 (1988)] PARAMETER BETA: 0.004200 CORRELATION ENERGY [LYP: C.L. LEE ET AL. PHYS. REV. B 37, 785 (1988)] *** DETSP| THE NEW SIZE OF THE PROGRAM IS 1716/ 49776 kBYTES *** >>>>>>>> CENTER OF MASS HAS BEEN MOVED TO CENTER OF BOX <<<<<<<< ***************************** ATOMS **************************** NR TYPE X(bohr) Y(bohr) Z(bohr) MBL 1 N 10.987436 13.131875 13.468706 3 2 C 13.438036 12.178637 14.828613 3 3 C 15.268374 14.655943 14.420429 3 4 O 17.266557 14.715263 15.633500 3 5 O 14.338897 16.170299 12.691970 3 6 H 11.969727 14.427276 12.175075 3 7 H 10.193959 14.506482 14.645546 3 8 H 9.725479 11.809643 12.888917 3 9 H 14.214852 10.617428 13.738530 3 10 H 12.991638 11.667640 16.764726 3 **************************************************************** NUMBER OF STATES: 15 NUMBER OF ELECTRONS: 30.00000 CHARGE: 0.00000 ELECTRON TEMPERATURE(KELVIN): 0.00000 OCCUPATION 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 ============================================================ | pseudopotential report: version 7.3.4 date 10-23-2003 | ------------------------------------------------------------ | nitrogen C-A + B88gx + LYPgc exchange-corr | | z = 7.00 zv = 5.00 exfact = 1.00000 | | etot = -19.28646 | | index orbital occupation energy | | 1 200 2.00 -1.35 | | 2 210 3.00 -0.52 | | keyps = 3 ifpcor = 0 | | rinner = 0.80 for L= 1 | | rinner = 0.80 for L= 2 | | rinner = 0.80 for L= 3 | | new generation scheme: | | nbeta = 4 kkbeta = 499 rcloc = 1.0000 | | ibeta l epsilon rcut iptype | | 1 0 -1.50 1.10 2 | | 2 0 0.00 1.10 2 | | 3 1 -0.70 1.10 2 | | 4 1 0.20 1.10 2 | | npf = 8 ptryc = 10.000 | | lloc = 2 eloc = 0.000 | | ifqopt = 3 nqf = 8 qtryc = 10.000 | | all electron calculation used schroedinger equation | | ************logarithmic mesh************ | ============================================================ ============================================================ | pseudopotential report: version 7.3.4 date 10-23-2003 | ------------------------------------------------------------ | carbon C-A + B88gx + LYPgc exchange-corr | | z = 6.00 zv = 4.00 exfact = 1.00000 | | etot = -10.70828 | | index orbital occupation energy | | 1 200 2.00 -1.00 | | 2 210 2.00 -0.38 | | keyps = 3 ifpcor = 0 | | rinner = 0.80 for L= 1 | | rinner = 0.80 for L= 2 | | rinner = 0.80 for L= 3 | | new generation scheme: | | nbeta = 4 kkbeta = 491 rcloc = 1.0000 | | ibeta l epsilon rcut iptype | | 1 0 -1.20 1.10 2 | | 2 0 0.20 1.10 2 | | 3 1 -0.60 1.10 2 | | 4 1 0.20 1.10 2 | | npf = 8 ptryc = 10.000 | | lloc = 2 eloc = 0.000 | | ifqopt = 3 nqf = 8 qtryc = 10.000 | | all electron calculation used schroedinger equation | | ************logarithmic mesh************ | ============================================================ ============================================================ | pseudopotential report: version 7.3.4 date 2- 3-2004 | ------------------------------------------------------------ | oxygen C-A + B88gx + LYPgc exchange-corr | | z = 8.00 zv = 6.00 exfact = 1.00000 | | etot = -31.57898 | | index orbital occupation energy | | 1 200 2.00 -1.75 | | 2 210 4.00 -0.66 | | keyps = 3 ifpcor = 0 | | rinner = 0.80 for L= 1 | | rinner = 0.80 for L= 2 | | rinner = 0.80 for L= 3 | | new generation scheme: | | nbeta = 4 kkbeta = 507 rcloc = 1.0000 | | ibeta l epsilon rcut iptype | | 1 0 -1.75 1.20 2 | | 2 0 -0.20 1.20 2 | | 3 1 -0.80 1.20 2 | | 4 1 0.20 1.20 2 | | npf = 8 ptryc = 10.000 | | lloc = 2 eloc = 0.000 | | ifqopt = 3 nqf = 8 qtryc = 10.000 | | all electron calculation used schroedinger equation | | ************logarithmic mesh************ | ============================================================ ============================================================ | pseudopotential report: version 7.3.4 date 10-23-2003 | ------------------------------------------------------------ | hydrogen C-A + B88gx + LYPgc exchange-corr | | z = 1.00 zv = 1.00 exfact = 1.00000 | | etot = -0.92437 | | index orbital occupation energy | | 1 100 1.00 -0.48 | | keyps = 3 ifpcor = 0 | | rinner = 0.80 for L= 1 | | new generation scheme: | | nbeta = 1 kkbeta = 371 rcloc = 0.8000 | | ibeta l epsilon rcut iptype | | 1 0 -0.48 0.80 2 | | npf = 6 ptryc = 10.000 | | lloc = 1 eloc = 0.000 | | ifqopt = 3 nqf = 8 qtryc = 10.000 | | all electron calculation used schroedinger equation | | ************logarithmic mesh************ | ============================================================ **************************************************************** * ATOM MASS RAGGIO NLCC PSEUDOPOTENTIAL * * N 14.0067 1.2000 NO VANDERBILT * * C 12.0112 1.2000 NO VANDERBILT * * O 15.9994 1.2000 NO VANDERBILT * * H 1.0080 1.2000 NO VANDERBILT * **************************************************************** OPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPEN NUMBER OF CPUS PER TASK 1 OPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPEN *** RGGEN| THE NEW SIZE OF THE PROGRAM IS 19608/ 79524 kBYTES *** ************************** SUPERCELL *************************** THIS IS AN ISOLATED SYSTEM CALCULATION POISSON EQUATION SOLVER : TUCKERMAN & MARTYNA SHORT RANGE POTENTIAL LENGTH * BOX LENGTH 7.000 SYMMETRY: SIMPLE CUBIC LATTICE CONSTANT(a.u.): 28.34589 CELL DIMENSION: 28.3459 1.0000 1.0000 0.0000 0.0000 0.0000 VOLUME(OMEGA IN BOHR^3): 22775.62400 LATTICE VECTOR A1(BOHR): 28.3459 0.0000 0.0000 LATTICE VECTOR A2(BOHR): 0.0000 28.3459 0.0000 LATTICE VECTOR A3(BOHR): 0.0000 0.0000 28.3459 RECIP. LAT. VEC. B1(2Pi/BOHR): 0.0353 0.0000 0.0000 RECIP. LAT. VEC. B2(2Pi/BOHR): 0.0000 0.0353 0.0000 RECIP. LAT. VEC. B3(2Pi/BOHR): 0.0000 0.0000 0.0353 REAL SPACE MESH: 108 108 108 WAVEFUNCTION CUTOFF(RYDBERG): 25.00000 DENSITY CUTOFF(RYDBERG): (DUAL= 5.00) 125.00000 NUMBER OF PLANE WAVES FOR WAVEFUNCTION CUTOFF: 23969 NUMBER OF PLANE WAVES FOR DENSITY CUTOFF: 268677 **************************************************************** *** RINFORCE| THE NEW SIZE OF THE PROGRAM IS 65440/ 134796 kBYTES *** *** FFTPRP| THE NEW SIZE OF THE PROGRAM IS 103560/ 159344 kBYTES *** *** CLUSTER| THE NEW SIZE OF THE PROGRAM IS 107820/ 163544 kBYTES *** *** NOSALLOC| THE NEW SIZE OF THE PROGRAM IS 107828/ 163544 kBYTES *** GENERATE ATOMIC BASIS SET N SLATER ORBITALS 2S ALPHA= 1.9237 OCCUPATION= 2.00 2P ALPHA= 1.9170 OCCUPATION= 3.00 C SLATER ORBITALS 2S ALPHA= 1.6083 OCCUPATION= 2.00 2P ALPHA= 1.5679 OCCUPATION= 2.00 O SLATER ORBITALS 2S ALPHA= 2.2458 OCCUPATION= 2.00 2P ALPHA= 2.2266 OCCUPATION= 4.00 H SLATER ORBITALS 1S ALPHA= 1.0000 OCCUPATION= 1.00 INITIALIZATION TIME: 11.19 SECONDS *** MDPT| THE NEW SIZE OF THE PROGRAM IS 108300/ 187288 kBYTES *** NOSEPA| TOTAL # OF ELECTRONIC DEGREES OF FREEDOM: 719040 NOSEPA| USED # OF ELECTRONIC DEGREES OF FREEDOM : 90 RESTART INFORMATION READ ON FILE ./RESTART *** PHFAC| THE NEW SIZE OF THE PROGRAM IS 119796/ 318164 kBYTES *** **************************************************************** * ATOMIC COORDINATES * **************************************************************** 1 N 10.892391 13.108611 13.738458 2 C 13.385995 12.215069 14.668606 3 C 15.243338 14.430710 14.431737 4 O 17.171458 14.823837 15.694407 5 O 14.524857 16.220199 12.542552 6 H 12.858927 15.733331 12.121383 7 H 9.600584 13.385277 15.133760 8 H 10.133713 11.696908 12.608707 9 H 13.954923 10.563967 13.517303 10 H 13.358951 11.749606 16.646955 **************************************************************** DEGREES OF FREEDOM FOR SYSTEM: 27 EWALD| SUM IN REAL SPACE OVER 1* 1* 1 CELLS **************************************************************** * ATOMIC COORDINATES * **************************************************************** 1 N 10.892391 13.108611 13.738458 2 C 13.385995 12.215069 14.668606 3 C 15.243338 14.430710 14.431737 4 O 17.171458 14.823837 15.694407 5 O 14.524857 16.220199 12.542552 6 H 12.858927 15.733331 12.121383 7 H 9.600584 13.385277 15.133760 8 H 10.133713 11.696908 12.608707 9 H 13.954923 10.563967 13.517303 10 H 13.358951 11.749606 16.646955 **************************************************************** CPU TIME FOR INITIALIZATION: 17.00 SECONDS ATOM COORDINATES GRADIENTS (-FORCES) 1 N 10.8909 13.1080 13.7388 -1.100E-02 -2.181E-02 -1.853E-02 2 C 13.3859 12.2143 14.6696 -1.293E-03 1.343E-02 -7.557E-03 3 C 15.2428 14.4303 14.4311 2.944E-02 3.338E-02 -7.887E-03 4 O 17.1712 14.8245 15.6937 -2.612E-02 -1.580E-02 -1.415E-02 5 O 14.5269 16.2215 12.5430 4.391E-02 -9.010E-03 2.947E-02 6 H 12.8578 15.7333 12.1210 -4.097E-02 -9.397E-03 -1.259E-02 7 H 9.6010 13.3831 15.1321 -1.322E-03 3.232E-03 7.323E-03 8 H 10.1352 11.6948 12.6085 -6.380E-05 9.002E-03 3.470E-03 9 H 13.9544 10.5608 13.5163 5.307E-03 5.566E-03 5.349E-03 10 H 13.3587 11.7498 16.6457 4.141E-04 -9.294E-03 1.265E-02 TOTAL INTEGRATED ELECTRONIC DENSITY IN G-SPACE = 30.000000 IN R-SPACE = 30.000000 VANDERBILT AUGMENTATION CHARGES (MEAN VALUE PER ATOM) ATOM TYPE NR. OF ATOMS CHARGE N 1 0.304 C 2 0.105 O 2 0.809 H 5 0.032 (K+E1+L+N+X) TOTAL ENERGY = -56.22279678 A.U. (K) KINETIC ENERGY = 28.27127461 A.U. (E1=A-S+R) ELECTROSTATIC ENERGY = -41.18447159 A.U. (S) ESELF = 44.54855464 A.U. (R) ESR = 2.32493454 A.U. (L) LOCAL PSEUDOPOTENTIAL ENERGY = -41.90110919 A.U. (N) N-L PSEUDOPOTENTIAL ENERGY = 13.21713102 A.U. (X) EXCHANGE-CORRELATION ENERGY = -14.62562164 A.U. GRADIENT CORRECTION ENERGY = -0.73486936 A.U. NFI EKINC TEMPP EKS ECLASSIC EHAM DIS TCPU 1 0.00076 275.6 -56.22280 -56.20936 -56.20860 0.407E-05 16.97 2 0.00074 277.6 -56.22287 -56.20934 -56.20860 0.162E-04 17.16 3 0.00074 279.6 -56.22296 -56.20934 -56.20860 0.364E-04 17.03 4 0.00075 281.4 -56.22305 -56.20935 -56.20860 0.645E-04 16.99 5 0.00078 283.1 -56.22314 -56.20938 -56.20860 0.101E-03 17.06 6 0.00081 284.7 -56.22322 -56.20941 -56.20860 0.145E-03 17.25 7 0.00084 286.3 -56.22330 -56.20944 -56.20860 0.197E-03 17.04 8 0.00087 287.9 -56.22338 -56.20947 -56.20860 0.257E-03 16.98 9 0.00089 289.5 -56.22345 -56.20949 -56.20860 0.325E-03 16.99 10 0.00090 291.1 -56.22351 -56.20950 -56.20860 0.400E-03 17.00 11 0.00091 292.8 -56.22356 -56.20951 -56.20860 0.484E-03 16.98 12 0.00091 294.5 -56.22360 -56.20951 -56.20860 0.576E-03 17.13 13 0.00090 296.1 -56.22363 -56.20950 -56.20860 0.675E-03 17.02 14 0.00089 297.5 -56.22365 -56.20950 -56.20860 0.783E-03 17.02 15 0.00089 298.7 -56.22366 -56.20949 -56.20860 0.898E-03 17.17 16 0.00088 299.6 -56.22366 -56.20948 -56.20860 0.102E-02 17.01 17 0.00088 300.3 -56.22365 -56.20948 -56.20860 0.115E-02 17.19 **************************************************************** * * * CPMD RECEIVED THE SOFT EXIT REQUEST * * THE COMMAND WAS ISSUED AT Wed Jan 5 18:53:19 2005 * * * **************************************************************** RESTART INFORMATION WRITTEN ON FILE ./RESTART.1 **************************************************************** * AVERAGED QUANTITIES * **************************************************************** MEAN VALUE +/- RMS DEVIATION [-^2]**(1/2) ELECTRON KINETIC ENERGY 0.843576E-03 0.620984E-04 IONIC TEMPERATURE 289.19 7.76 DENSITY FUNCTIONAL ENERGY -56.223357 0.289683E-03 CLASSICAL ENERGY -56.209445 0.627254E-04 CONSERVED ENERGY -56.208601 0.953674E-06 NOSE ENERGY ELECTRONS 0.001216 0.629773E-04 NOSE ENERGY IONS 0.000333 0.164197E-03 CONSTRAINTS ENERGY 0.000000 0.00000 ION DISPLACEMENT 0.419469E-03 0.361323E-03 CPU TIME 17.0582 **************************************************************** * * * FINAL RESULTS * * * **************************************************************** **************************************************************** * ATOMIC COORDINATES * **************************************************************** 1 N 10.867913 13.097486 13.741872 2 C 13.383748 12.203434 14.683907 3 C 15.237619 14.426779 14.420489 4 O 17.165984 14.832793 15.682723 5 O 14.559629 16.239675 12.550868 6 H 12.809076 15.725986 12.104377 7 H 9.602015 13.355044 15.118684 8 H 10.156727 11.672262 12.609520 9 H 13.951234 10.522358 13.508434 10 H 13.355318 11.742627 16.642717 **************************************************************** **************************************************************** ELECTRONIC GRADIENT: MAX. COMPONENT = 6.30508E-04 NORM = 4.90877E-05 TOTAL INTEGRATED ELECTRONIC DENSITY IN G-SPACE = 30.000000 IN R-SPACE = 30.000000 VANDERBILT AUGMENTATION CHARGES (MEAN VALUE PER ATOM) ATOM TYPE NR. OF ATOMS CHARGE N 1 0.304 C 2 0.104 O 2 0.805 H 5 0.031 (K+E1+L+N+X) TOTAL ENERGY = -56.22364859 A.U. (K) KINETIC ENERGY = 28.21497176 A.U. (E1=A-S+R) ELECTROSTATIC ENERGY = -41.26392863 A.U. (S) ESELF = 44.54855464 A.U. (R) ESR = 2.25236016 A.U. (L) LOCAL PSEUDOPOTENTIAL ENERGY = -41.76914780 A.U. (N) N-L PSEUDOPOTENTIAL ENERGY = 13.19860743 A.U. (X) EXCHANGE-CORRELATION ENERGY = -14.60415136 A.U. GRADIENT CORRECTION ENERGY = -0.73435819 A.U. **************************************************************** ================================================================ BIG MEMORY ALLOCATIONS SCR 7012699 EIGRB 5373540 YF 2590058 PSI 2590058 VR 2590058 XF 2590058 YLMB 2418093 QRAD 1527840 QRL 1454400 RHOE 1295029 ---------------------------------------------------------------- [PEAK NUMBER 113] PEAK MEMORY 34632748 = 277.1 MBytes ================================================================ **************************************************************** * * * TIMING * * * **************************************************************** SUBROUTINE CALLS CPU TIME ELAPSED TIME NEWD 18 98.75 98.74 RHOV 18 38.27 38.31 S_INVFFT 288 24.62 24.69 GCENER 18 20.19 20.21 FWFFT 109 18.07 17.98 INVFFT 90 14.62 14.58 XCENER 18 13.80 13.83 RNLSM2 18 12.99 18.74 S_FWFFT 144 11.58 11.64 FFT-G/S 864 10.68 10.56 QINIT 1 8.80 8.80 RNLSM1 36 8.16 12.05 VPSI 18 6.67 6.61 RHOOFR 18 6.52 6.60 NLFORCE 18 5.11 5.12 PHASE 199 3.35 3.41 VOFRHOT 18 2.61 2.61 EICALC 18 2.56 2.56 GRADEN 18 2.49 2.50 ROTATE 109 1.44 1.45 PHFAC 18 1.19 1.23 VOFRHOB 18 1.17 1.21 VDBINIT 4 1.11 1.11 ---------------------------------------------------------------- TOTAL TIME 314.75 324.55 **************************************************************** CPU TIME : 0 HOURS 5 MINUTES 18.40 SECONDS ELAPSED TIME : 0 HOURS 5 MINUTES 30.00 SECONDS PROGRAM CPMD ENDED AT: Wed Jan 5 18:53:21 2005 **************************************************************** * * * CPMD RECEIVED THE SOFT EXIT REQUEST * * THE COMMAND WAS ISSUED AT Wed Jan 5 18:53:21 2005 * * * ****************************************************************