cp2k fails to compute atomic forces
Kristof
kristof... at googlemail.com
Wed Nov 28 17:54:26 UTC 2012
Hi,
I'm using cp2k to compute MD trajectories with DFTB with two different
system setups. On both systems I encountered the same error, yet they
occured at different stages of the calculations
System 1 worked fine when the calculations were started from scratch, but
failed when I attempted to restart the system. However, if I use the
restart file as the input file, the calculations work just fine.
System 2 already tends to fail when starting from scratch, but casually
works when the number of processors cp2k runs on is varied.
Calculations that fail usually manage to compute the SCF Energy but then
fail to calculate the forces (NaN in one or two colums, see appendiy). The
program eventually exits with the following error:
*****************************************************************************
*** 17:30:26 ERRORL2 in cp_fm_cholesky:cp_fm_cholesky_decompose processor
***
*** 0 err=-300 condition FAILED at line 102
***
*****************************************************************************
My question now is: What are the roots of the problem and how do I get
around it without having to try every possible combination of mpi, cp2k
version and processor number.
Many thanks in advance,
best,
Kristof
The input and corresponding output files are as follows: (Complete outputs
(input, output, coordinates etc... are attached)
System 1:
========================================================================================
Input:
&GLOBAL
PROJECT gp-MD_235
WALLTIME 35500 #10h
RUN_TYPE MD
PRINT_LEVEL HIGH
&END GLOBAL
&EXT_RESTART
RESTART_FILE_NAME gp-MD_235-1.restart
&END EXT_RESTART
&MOTION
&CONSTRAINT
&COLLECTIVE
COLVAR 1
TARGET [angstrom] 2.35
INTERMOLECULAR TRUE
&END COLLECTIVE
&COLLECTIVE
COLVAR 2
TARGET [angstrom] 2.35
INTERMOLECULAR TRUE
&END COLLECTIVE
&LAGRANGE_MULTIPLIERS
FILENAME =gp-MD_235.lag
&END LAGRANGE_MULTIPLIERS
&END CONSTRAINT
&MD
ENSEMBLE NVT
STEPS 1
TIMESTEP 0.5
TEMPERATURE 300.0
&THERMAL_REGION
FORCE_RESCALING
&DEFINE_REGION
LIST 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24
25 26 27 28 29 30 31
TEMP_TOL 200
TEMPERATURE 300.0
&END DEFINE_REGION
&END THERMAL_REGION
&THERMOSTAT
REGION GLOBAL
TYPE CSVR
&CSVR
TIMECON=25.0
&END CSVR
&END THERMOSTAT
&END MD
&PRINT
&TRAJECTORY
# SECTION_PARAMETERS LOW
UNIT angstrom
FORMAT XYZ
&EACH
MD 100
&END EACH
&END TRAJECTORY
&VELOCITIES
# SECTION_PARAMETERS HIGH
UNIT angstrom*fs^-1
FORMAT XYZ
&EACH
MD 10
&END EACH
&END VELOCITIES
&RESTART
BACKUP_COPIES 0
&EACH
MD 1
&END EACH
&END RESTART
&STRUCTURE_DATA
DISTANCE 1 19
DISTANCE 2 17
FILENAME =gp-MD_235.dist
&END STRUCTURE_DATA
&END PRINT
&END MOTION
&FORCE_EVAL
&DFT
&QS
METHOD DFTB
&DFTB
DO_EWALD T
SELF_CONSISTENT T
DISPERSION F
HB_SR_GAMMA F
&PARAMETER
PARAM_FILE_PATH /project/hydroqmd/karhan/DFTB_Potentials
SK_FILE H H hh.spl
SK_FILE O O oo_modi.spl
SK_FILE H O ho_modi.spl
SK_FILE O H oh_modi.spl
SK_FILE H C hc.spl
SK_FILE H N hn_modi.spl
SK_FILE O C oc.spl
SK_FILE O N on.spl
SK_FILE C C cc.spl
SK_FILE C H ch.spl
SK_FILE C O co.spl
SK_FILE C N cn.spl
SK_FILE N N nn.spl
SK_FILE N H nh_modi.spl
SK_FILE N O no.spl
SK_FILE N C nc.spl
UFF_FORCE_FIELD ./uff_table
&END PARAMETER
&END DFTB
EXTRAPOLATION ASPC
EXTRAPOLATION_ORDER 3 #0
&END QS
&SCF
SCF_GUESS ATOMIC
EPS_SCF 25.0E-6
MAX_SCF 30
#CHOLESKY OFF
&OT ON
MINIMIZER DIIS
PRECONDITIONER FULL_SINGLE_INVERSE
STEPSIZE 0.125
&END OT
&OUTER_SCF
TYPE NONE
OPTIMIZER NONE
EPS_SCF 25.0E-6
MAX_SCF 25
&END OUTER_SCF
&PRINT
&RESTART
BACKUP_COPIES 0
&EACH
MD 10
QS_SCF 0
&END EACH
&END RESTART
&RESTART_HISTORY OFF
&END RESTART_HISTORY
&END PRINT
&END SCF
&POISSON
PERIODIC XYZ
POISSON_SOLVER PERIODIC
&EWALD
EWALD_TYPE SPME
GMAX 64 64 64
O_SPLINE 8
&END EWALD
&END POISSON
&END DFT
&SUBSYS
&CELL
ABC 50.0 50.0 50.0
PERIODIC XYZ
&END CELL
&TOPOLOGY
COORD_FILE_NAME 235pm.xyz
COORDINATE XYZ
&END TOPOLOGY
&COLVAR
&DISTANCE
ATOMS 1 19
&END DISTANCE
&END COLVAR
&COLVAR
&DISTANCE
ATOMS 2 17
&END DISTANCE
&END COLVAR
&END SUBSYS
# STRESS_TENSOR ANALYTICAL
&END FORCE_EVAL
*#EOF*
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Restart file:
&GLOBAL
PRINT_LEVEL MEDIUM
PROJECT_NAME gp-MD_235
RUN_TYPE MD
WALLTIME 4.3200000000000000E+04
&END GLOBAL
&MOTION
&MD
ENSEMBLE NVT
STEPS 140000
TIMESTEP 4.9999999999999994E-01
STEP_START_VAL 24429
TIME_START_VAL 1.2214500000006783E+04
ECONS_START_VAL -4.2053706025519297E+01
TEMPERATURE 3.0000000000000000E+02
&THERMOSTAT
TYPE CSVR
REGION GLOBAL
&CSVR
TIMECON 2.4999999999999996E+01
&THERMOSTAT_ENERGY
-2.9219349520992220E-02
&END THERMOSTAT_ENERGY
&RNG_INIT
Wiener process for Thermostat # 1 1 F T F
1.4628890444211335E+00 3475418064.0 1716988953.0
4215312644.0 914178388.0 2784134980.0
1923055373.0 12345.0 12345.0
12345.0 12345.0 12345.0
12345.0 12345.0 12345.0
12345.0 12345.0 12345.0 12345.0
&END RNG_INIT
&END CSVR
&END THERMOSTAT
&AVERAGES T
&RESTART_AVERAGES
ITIMES_START 1
AVECPU 1.4739436735028089E+00
AVEHUGONIOT 0.0000000000000000E+00
AVETEMP_BARO 0.0000000000000000E+00
AVEPOT -4.2136485328389085E+01
AVEKIN 4.1852645851588807E-02
AVETEMP 3.0036373880890966E+02
AVEKIN_QM 0.0000000000000000E+00
AVETEMP_QM 0.0000000000000000E+00
AVEVOL 8.4354182288623450E+05
AVECELL_A 9.4486306644281925E+01
AVECELL_B 9.4486306644281925E+01
AVECELL_C 9.4486306644281925E+01
AVEALPHA 9.0000000000000028E+01
AVEBETA 9.0000000000000028E+01
AVEGAMMA 9.0000000000000028E+01
AVE_ECONS -6.7503303929371612E+01
AVE_PRESS 0.0000000000000000E+00
AVE_PXX 0.0000000000000000E+00
&END RESTART_AVERAGES
&END AVERAGES
&THERMAL_REGION
FORCE_RESCALING T
&DEFINE_REGION
LIST 1 2 3
4 5 6 7 \
8 9 10
11 12 13 14 15 \
16 17 18
19 20 21 22 23 \
24 25 26
27 28 29 30 31
TEMPERATURE 3.0000000000000000E+02
TEMP_TOL 1.5000000000000000E+02
&END DEFINE_REGION
&END THERMAL_REGION
&END MD
&CONSTRAINT
&COLLECTIVE
COLVAR 1
INTERMOLECULAR T
TARGET 4.4408564122812608E+00
&END COLLECTIVE
&COLLECTIVE
COLVAR 2
INTERMOLECULAR T
TARGET 4.4408564122812608E+00
&END COLLECTIVE
&LAGRANGE_MULTIPLIERS SILENT
FILENAME =gp-MD_235.lag
&END LAGRANGE_MULTIPLIERS
&END CONSTRAINT
&PRINT
&TRAJECTORY SILENT
UNIT angstrom
FORMAT XMOL
&EACH
MD 100
&END EACH
&END TRAJECTORY
&VELOCITIES SILENT
UNIT angstrom*fs^-1
FORMAT XMOL
&EACH
MD 10
&END EACH
&END VELOCITIES
&STRUCTURE_DATA SILENT
FILENAME =gp-MD_235.dist
DISTANCE 1 19
DISTANCE 2 17
&END STRUCTURE_DATA
&RESTART SILENT
BACKUP_COPIES 0
&EACH
MD 1
&END EACH
&END RESTART
&END PRINT
&END MOTION
&FORCE_EVAL
&DFT
&SCF
MAX_SCF 30
EPS_SCF 2.5000000000000001E-05
SCF_GUESS ATOMIC
&OT T
MINIMIZER DIIS
STEPSIZE 1.2500000000000000E-01
PRECONDITIONER FULL_SINGLE_INVERSE
&END OT
&OUTER_SCF T
TYPE NONE
OPTIMIZER NONE
EPS_SCF 2.5000000000000001E-05
MAX_SCF 25
&END OUTER_SCF
&PRINT
&RESTART SILENT
BACKUP_COPIES 0
&EACH
QS_SCF 0
MD 10
&END EACH
&END RESTART
&RESTART_HISTORY OFF
&END RESTART_HISTORY
&END PRINT
&END SCF
&QS
EXTRAPOLATION ASPC
EXTRAPOLATION_ORDER 3
METHOD DFTB
&DFTB
SELF_CONSISTENT T
DO_EWALD T
DISPERSION F
HB_SR_GAMMA F
&PARAMETER
SK_FILE H H hh.spl
SK_FILE O O oo_modi.spl
SK_FILE H O ho_modi.spl
SK_FILE O H oh_modi.spl
SK_FILE H C hc.spl
SK_FILE H N hn_modi.spl
SK_FILE O C oc.spl
SK_FILE O N on.spl
SK_FILE C C cc.spl
SK_FILE C H ch.spl
SK_FILE C O co.spl
SK_FILE C N cn.spl
SK_FILE N N nn.spl
SK_FILE N H nh_modi.spl
SK_FILE N O no.spl
SK_FILE N C nc.spl
PARAM_FILE_PATH /project/hydroqmd/karhan/DFTB_Potentials
UFF_FORCE_FIELD ./uff_table
&END PARAMETER
&END DFTB
&END QS
&POISSON
POISSON_SOLVER PERIODIC
PERIODIC XYZ
&EWALD
EWALD_TYPE SPME
GMAX 64 64 64
O_SPLINE 8
&END EWALD
&END POISSON
&END DFT
&SUBSYS
&CELL
A 5.0000000000000007E+01 0.0000000000000000E+00
0.0000000000000000E+00
B 0.0000000000000000E+00 5.0000000000000007E+01
0.0000000000000000E+00
C 0.0000000000000000E+00 0.0000000000000000E+00
5.0000000000000007E+01
PERIODIC XYZ
MULTIPLE_UNIT_CELL 1 1 1
&END CELL
&COORD
N 6.4863600238239014E+00 7.9452958208669209E+00
4.3811519133811743E+00
N 6.4817443214184456E+00 8.9492944923911804E+00
5.1875003519654053E+00
C 7.3702837323744204E+00 8.3510844411529881E+00
3.2750189875670945E+00
O 7.5914884553446536E+00 7.5835865377744716E+00
2.3256436134573133E+00
O 7.8038432189815330E+00 9.6470615445280590E+00
3.2957387593786471E+00
C 5.2966361697764661E+00 8.7635096279154379E+00
6.0879785246984985E+00
O 5.4223103070358940E+00 8.3471836533820483E+00
7.2429722983093150E+00
O 4.2278284203415577E+00 9.2217842226229418E+00
5.4727761414753395E+00
C 8.5774950357864572E+00 9.8758032619614511E+00
2.1602958118292794E+00
H 9.4259446563875855E+00 1.0544105803141415E+01
2.3020923828630799E+00
H 8.1150524307825567E+00 1.0491990498402613E+01
1.3437395214263403E+00
H 8.9608537662464833E+00 8.9046038681123481E+00
1.6995822382638803E+00
C 3.1572303067817855E+00 9.5591918465029320E+00
6.4124664969969984E+00
H 3.5101533861302410E+00 1.0371862975053077E+01
7.0695470825594260E+00
H 2.8793773250950592E+00 8.6659415560324664E+00
7.0375952252716747E+00
H 2.3010145326258247E+00 9.9018010376686654E+00
5.7747120599502626E+00
C 8.1571839790278489E+00 8.0737143833624909E+00
6.5834813125921672E+00
H 7.0804373019682068E+00 6.3867362620413433E+00
5.5610965902309095E+00
C 8.0285215871959164E+00 6.8217807256907399E+00
5.7529943357120761E+00
C 9.5729117672058504E+00 8.6453887469255992E+00
6.2694870647359746E+00
H 9.8659076182145640E+00 9.6776331319193289E+00
6.5669459277751256E+00
C 9.3137787937986936E+00 6.7800703415764216E+00
4.9940195489849764E+00
H 9.3676542064073907E+00 6.0942922775424213E+00
4.1601291463034489E+00
C 9.2509797486619867E+00 6.2135605638778060E+00
6.4020780348033890E+00
H 9.4451128627729837E+00 5.2291382672941307E+00
6.8717049552367095E+00
C 9.4897728798682515E+00 7.5067645805415495E+00
7.2050860086035522E+00
H 9.5955395563849191E+00 7.5857485813431413E+00
8.2587574870627787E+00
C 9.9900742917113714E+00 8.1512651643818295E+00
4.9369522860695945E+00
H 1.1079527194924999E+01 7.9551265322224332E+00
5.1201021184562912E+00
H 9.8822230615353863E+00 8.9468996329368746E+00
4.1833081884005665E+00
H 7.4943003234676606E+00 8.4957468855948886E+00
7.3459272740077433E+00
&END COORD
&VELOCITY
-5.4464047916049728E-05 5.0701275473243078E-04
1.4865379449609364E-04
-2.5290376227568389E-04 -6.4696131246640650E-05
2.1161162407736534E-04
-1.8241501200286838E-04 1.2759423849687172E-04
-6.7863000610037314E-05
1.2348408062068245E-04 -1.1159317965976608E-04
3.8602275835755695E-04
-2.9568145976398378E-06 -1.9173940006441157E-04
-2.2988677664155545E-05
-4.9213361144708140E-04 2.4215013200921623E-04
2.2059691338757742E-04
2.9064396154276256E-04 3.6459206560567002E-05
-2.7442762707431011E-04
-7.4568861262718406E-05 1.2270009700022567E-04
-6.0263619973598273E-05
2.2360259562425642E-04 -3.6439199948875195E-04
4.3194237040178817E-04
5.6144050914807913E-04 4.4836098159556440E-04
-7.3570131818170023E-04
-1.3338709004666704E-03 -6.9848566396243870E-05
-3.2486777962354693E-04
-1.4464022629033903E-03 5.4936251424604371E-04
-1.9611387623248338E-03
2.1582183658771460E-04 -9.0834591612543939E-05
6.8509521953965622E-05
5.3956123275813528E-04 2.0282001400137180E-04
5.3224662655143923E-05
-2.8823764910735500E-04 -5.2237448542059243E-04
-7.4690506308711026E-04
5.5441385132571860E-04 -5.7731293914302644E-04
8.9177860285717843E-04
7.7623745111323714E-05 -6.6421453571909150E-05
-1.8616568620008554E-04
5.5637524505931693E-04 3.3141700409184397E-04
-8.2971829406330361E-05
-2.4024192521236612E-04 -1.7357121282885130E-04
-1.9988977845039241E-04
4.3204225595278090E-05 3.7231299827716543E-06
-3.3443532870428591E-04
-3.3120349640486542E-04 1.8874642836182542E-04
-6.0979211559954399E-04
-1.0888136750200859E-04 -1.7706813569056033E-04
4.2035601936126370E-05
-9.9251102207241352E-04 1.1633550850525009E-04
-2.0490479674692042E-03
-4.4669392430647584E-05 -2.4628486416057295E-04
-9.6711968393699461E-05
1.2314151225628295E-03 1.0861563982543529E-03
-6.6449228186268947E-04
2.3112571564821251E-05 2.4241699421019363E-04
-7.9311927159056446E-06
-1.5846131258884669E-03 1.1692160493469968E-04
5.3410311720093859E-04
5.8908914332580521E-04 1.2461706608152737E-04
1.3525499103248984E-04
-1.0570722959344367E-03 -1.0959582962172501E-04
-6.8061819778573020E-04
8.5893117056819971E-04 8.3215539155862285E-05
-3.9538049723051189E-04
4.1943881318544835E-04 -1.1971583367067248E-03
1.2518734284727793E-03
&END VELOCITY
&TOPOLOGY
COORD_FILE_NAME 235pm.xyz
COORD_FILE_FORMAT XYZ
NUMBER_OF_ATOMS 31
MULTIPLE_UNIT_CELL 1 1 1
&END TOPOLOGY
&COLVAR
&DISTANCE
ATOMS 1 19
&END DISTANCE
&END COLVAR
&COLVAR
&DISTANCE
ATOMS 2 17
&END DISTANCE
&END COLVAR
&END SUBSYS
&END FORCE_EVAL
*#EOF*
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Output:
[...]
*** SCF run converged in 7 steps ***
Core Hamiltonian energy:
-43.37182167916384
Repulsive potential energy:
1.17589868046140
Electronic energy:
0.06298606193450
Dispersion energy:
0.00000000000000
Total energy:
-42.13293693676793
outer SCF iter = 2 RMS gradient = 0.24E-04 energy =
-42.1329369368
outer SCF loop converged in 2 iterations or 37 steps
Repulsive pair potential energy:
1.1758986805
Zeroth order Hamiltonian energy:
-43.3718318718
Charge fluctuation energy:
0.0629956753
London dispersion energy:
0.0000000000
FORCES [a.u.]
Atom Kind Component X Y Z
1 1 all_potential -0.273151 -0.835888 -0.227235
1 1 overlap 0.188408 0.462566 0.107691
1 1 overlap_admm 0.000000 0.000000 0.000000
1 1 rho_elec NaN NaN 0.010310
1 1 repulsive 0.069008 0.319909 0.142989
1 1 dispersion 0.000000 0.000000 0.000000
1 1 total NaN NaN 0.033756
[...]
Sum of total NaN NaN -0.000000
ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.):
-42.132937515994506
ATOMIC FORCES in [a.u.]
# Atom Kind Element X Y Z
1 1 N NaN NaN -0.03375607
2 1 N NaN NaN 0.01464264
3 2 C NaN NaN -0.02850964
4 3 O NaN NaN 0.03379040
5 3 O NaN NaN -0.00238376
[...]
SUM OF ATOMIC FORCES NaN NaN
0.00000000 NaN
MD_ENERGIES| Initialization proceeding
******************************** GO CP2K GO!
**********************************
INITIAL POTENTIAL ENERGY[hartree] =
-0.421329375160E+02
INITIAL KINETIC ENERGY[hartree] =
0.441770740388E-01
INITIAL TEMPERATURE[K] =
317.045
INITIAL VOLUME[bohr^3] =
0.843541822886E+06
INITIAL CELL LNTHS[bohr] = 0.9448631E+02 0.9448631E+02
0.9448631E+02
INITIAL CELL ANGLS[deg] = 0.9000000E+02 0.9000000E+02
0.9000000E+02
******************************** GO CP2K GO!
**********************************
SHAKE_INFO| External Shake Nr. Iterations: 1 Max. Err.:
0.000000000
DISTRIBUTION OF THE NEIGHBOR LISTS
Total number of particle
pairs: 0
Total number of matrix
elements: 0
Average number of particle
pairs: 0
Maximum number of particle
pairs: 0
Average number of matrix
element: 0
Maximum number of matrix
elements: 0
Number of
electrons: 92
Number of occupied
orbitals: 46
Number of molecular
orbitals: 46
Number of orbital
functions: 82
Number of independent orbital
functions: 82
Parameters for the always stable predictor-corrector (ASPC) method:
ASPC order: 0
B(1) = 1.000000
*****************************************************************************
*** 17:30:26 ERRORL2 in cp_fm_cholesky:cp_fm_cholesky_decompose processor
***
*** 0 err=-300 condition FAILED at line 102
***
*****************************************************************************
===== Routine Calling Stack =====
11 cp_fm_cholesky_decompose
10 make_basis_sm
9 qs_env_reorthogonalize_vectors
8 wfi_extrapolate
7 scf_env_initial_rho_setup
6 init_scf_run
5 qs_energies_scf
4 qs_forces
3 velocity_verlet
2 qs_mol_dyn_low
1 CP2K
*#EOF*
===========================================================
System 2:
===========================================================
Input:
&GLOBAL
PROJECT iw-T_290
WALLTIME 7000 #sec
RUN_TYPE MD
PRINT_LEVEL HIGH
&END GLOBAL
@SET RE-START 0
#&EXT_RESTART
# RESTART_FILE_NAME iw-MD_290-1.restart
# @SET RE-START 1
#&END EXT_RESTART
&MOTION
&CONSTRAINT
&COLLECTIVE
COLVAR 1
TARGET [angstrom] 2.9
INTERMOLECULAR TRUE
&END COLLECTIVE
&COLLECTIVE
COLVAR 2
TARGET [angstrom] 2.9
INTERMOLECULAR TRUE
&END COLLECTIVE
&LAGRANGE_MULTIPLIERS
FILENAME =iw-MD_290.lag
&END LAGRANGE_MULTIPLIERS
&END CONSTRAINT
&MD
ENSEMBLE NVT
STEPS 050
TIMESTEP 0.5
TEMPERATURE 300.0
&THERMAL_REGION
FORCE_RESCALING
&DEFINE_REGION
LIST 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24
25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74
75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99
100
LIST 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116
117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135
136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154
155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173
174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192
193 194 195 196 197 198 199 200
LIST 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216
217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235
236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254
255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273
274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292
293 294 295 296 297 298 299 300
LIST 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316
317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335
336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354
355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373
374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392
393 394 395 396 397 398 399 400
LIST 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416
417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435
436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454
455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473
474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492
493 494 495 496 497 498 499 500
LIST 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516
517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535
536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554
555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573
574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592
593 594 595 596 597 598 599 600
LIST 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616
617 618 619 620 621 622 623 624 625 626 627 628 629 630 631
TEMP_TOL 150
TEMPERATURE 300.0
&END DEFINE_REGION
&END THERMAL_REGION
&THERMOSTAT
REGION GLOBAL
TYPE CSVR
&CSVR
TIMECON 25.0
&END CSVR
&END THERMOSTAT
&END MD
&PRINT
&TRAJECTORY
# SECTION_PARAMETERS LOW
UNIT angstrom
FORMAT XYZ
&EACH
MD 500
&END EACH
&END TRAJECTORY
&VELOCITIES
# SECTION_PARAMETERS HIGH
UNIT angstrom*fs^-1
FORMAT XYZ
&EACH
MD 10
&END EACH
&END VELOCITIES
&RESTART
BACKUP_COPIES 0
&EACH
MD 1
&END EACH
&END RESTART
&STRUCTURE_DATA
DISTANCE 601 619
DISTANCE 602 617
FILENAME =iw-MD_290.dist
&END STRUCTURE_DATA
&END PRINT
&END MOTION
&FORCE_EVAL
&DFT
&QS
METHOD DFTB
&DFTB
DO_EWALD T
SELF_CONSISTENT T
DISPERSION F
HB_SR_GAMMA F
&PARAMETER
PARAM_FILE_PATH /project/hydroqmd/karhan/DFTB_Potentials
SK_FILE H H hh.spl
SK_FILE O O oo_modi.spl
SK_FILE H O ho_modi.spl
SK_FILE O H oh_modi.spl
SK_FILE H C hc.spl
SK_FILE H N hn_modi.spl
SK_FILE O C oc.spl
SK_FILE O N on.spl
SK_FILE C C cc.spl
SK_FILE C H ch.spl
SK_FILE C O co.spl
SK_FILE C N cn.spl
SK_FILE N N nn.spl
SK_FILE N H nh_modi.spl
SK_FILE N O no.spl
SK_FILE N C nc.spl
UFF_FORCE_FIELD ./uff_table
&END PARAMETER
&END DFTB
EXTRAPOLATION ASPC
EXTRAPOLATION_ORDER 3 #0
&END QS
&SCF
@IF ${RE-START} == 1
SCF_GUESS ATOMIC
@ENDIF
@IF ${RE-START} /= 1
SCF_GUESS ATOMIC
@ENDIF
EPS_SCF 25.0E-6
MAX_SCF 30
&OT ON
MINIMIZER DIIS
PRECONDITIONER FULL_SINGLE_INVERSE
STEPSIZE 0.125
&END OT
&OUTER_SCF
TYPE NONE
OPTIMIZER NONE
EPS_SCF 25.0E-6
MAX_SCF 25
&END OUTER_SCF
&PRINT
&RESTART
BACKUP_COPIES 0
&END RESTART
&RESTART_HISTORY OFF
&END RESTART_HISTORY
&END PRINT
&END SCF
&POISSON
PERIODIC XYZ
POISSON_SOLVER PERIODIC
&EWALD
EWALD_TYPE SPME
GMAX 22 22 22
O_SPLINE 8
&END EWALD
&END POISSON
&END DFT
&SUBSYS
&CELL
ABC 18.5 18.5 18.5
PERIODIC XYZ
&END CELL
&TOPOLOGY
COORD_FILE_NAME 290pm.xyz
COORDINATE XYZ
&END TOPOLOGY
&COLVAR
&DISTANCE
ATOMS 601 619
&END DISTANCE
&END COLVAR
&COLVAR
&DISTANCE
ATOMS 602 617
&END DISTANCE
&END COLVAR
&END SUBSYS
# STRESS_TENSOR ANALYTICAL
&END FORCE_EVAL
*#EOF*
----------------------------------------------------------------------------------
Output:
[...]
*** SCF run converged in 7 steps ***
Core Hamiltonian energy:
-870.20346624911110
Repulsive potential energy:
14.53194654350423
Electronic energy:
4.55640608012233
Dispersion energy:
0.00000000000000
Total energy:
-851.11511362548458
outer SCF iter = 2 RMS gradient = 0.20E-04 energy =
-851.1151136255
outer SCF loop converged in 2 iterations or 37 steps
Repulsive pair potential energy:
14.5319465435
Zeroth order Hamiltonian energy:
-870.2041392509
Charge fluctuation energy:
4.5568602523
London dispersion energy:
0.0000000000
FORCES [a.u.]
Atom Kind Component X Y Z
1 1 all_potential -0.266485 0.249637 -0.056982
1 1 overlap 0.153856 -0.126249 0.036563
1 1 overlap_admm 0.000000 0.000000 0.000000
1 1 rho_elec NaN NaN 0.001861
1 1 repulsive 0.094985 -0.103863 0.015790
1 1 dispersion 0.000000 0.000000 0.000000
1 1 total NaN NaN -0.002769
[...]
Sum of total NaN NaN -0.000010
ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.):
-851.115332455143744
ATOMIC FORCES in [a.u.]
# Atom Kind Element X Y Z
1 1 H NaN NaN 0.00276854
2 1 H NaN NaN 0.00557624
3 2 O NaN NaN -0.00447146
4 1 H NaN NaN -0.00613486
5 1 H NaN NaN -0.01651623
[...]
SUM OF ATOMIC FORCES NaN NaN
0.00000956 NaN
MD_ENERGIES| Initialization proceeding
******************************** GO CP2K GO!
**********************************
INITIAL POTENTIAL ENERGY[hartree] =
-0.851115332455E+03
INITIAL KINETIC ENERGY[hartree] =
0.899217216726E+00
INITIAL TEMPERATURE[K] =
300.794
INITIAL VOLUME[bohr^3] =
0.427279239547E+05
INITIAL CELL LNTHS[bohr] = 0.3495993E+02 0.3495993E+02
0.3495993E+02
INITIAL CELL ANGLS[deg] = 0.9000000E+02 0.9000000E+02
0.9000000E+02
******************************** GO CP2K GO!
**********************************
*** 11:26:41 WARNING in md_energies:md_write_output The print_key ***
*** MD%PRINT%TEMP_KIND has been activated but the calculation of the ***
*** temperature per kind has not been requested. Please switch on the ***
*** keyword MD%TEMP_KIND. md_energies.F line 506 ***
SHAKE_INFO| External Shake Nr. Iterations: 1 Max. Err.:
0.000000000
DISTRIBUTION OF THE NEIGHBOR LISTS
Total number of particle
pairs: 0
Total number of matrix
elements: 0
Average number of particle
pairs: 0
Maximum number of particle
pairs: 0
Average number of matrix
element: 0
Maximum number of matrix
elements: 0
Number of electrons:
1692
Number of occupied
orbitals: 846
Number of molecular
orbitals: 846
Number of orbital functions:
1282
Number of independent orbital functions:
1282
Parameters for the always stable predictor-corrector (ASPC) method:
ASPC order: 0
B(1) = 1.000000
*****************************************************************************
*** 11:26:41 ERRORL2 in cp_fm_cholesky:cp_fm_cholesky_decompose processor
***
*** 0 err=-300 condition FAILED at line 102
***
*****************************************************************************
===== Routine Calling Stack =====
11 cp_fm_cholesky_decompose
10 make_basis_sm
9 qs_env_reorthogonalize_vectors
8 wfi_extrapolate
7 scf_env_initial_rho_setup
6 init_scf_run
5 qs_energies_scf
4 qs_forces
3 velocity_verlet
2 qs_mol_dyn_low
1 CP2K
*#EOF*
=========================================
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