[CP2K:3052] Error in fixing atomic positions during atomic relaxation?
Teodoro Laino
teodor... at gmail.com
Wed Jan 12 10:01:31 UTC 2011
Dear Valerio,
there is no bug. The line has clearly a fixed length and although you put all elements in a line there is no way that CP2K will read all of them.
Also, this NEVER worked before: we have always had the issue of a fixed buffer length.
The solution:
you can use the keyword LIST in a repeated fashion, in order no to have extremely long lines.
in your case:
&FIXED_ATOMS
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
LIST 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48
LIST 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71
LIST 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94
LIST 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113
LIST 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130
LIST 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147
LIST 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164
LIST 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181
LIST 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198
LIST 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215
LIST 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232
LIST 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249
LIST 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266
LIST 267 268 269 270
&END FIXED_ATOMS
it will work with your version without any need to recompile or update the source code.
Regards,
TL
On Jan 12, 2011, at 10:56 AM, Valerio Bellini wrote:
> Dear all,
>
> I am running the cp2k version of 30.11.2010.. (2.2.57),
> studying a system of > 500 atoms, and want to fix
> in their initial position part of the atoms, during a standard
> minimization procedure with DFT-QS.
> Here it is my input file (it needed I could also give the coordinates, but
> I guess the problems happens for whatsoever coordinates)
>
> &GLOBAL
> PROJECT ./working
> RUN_TYPE GEO_OPT
> PRINT_LEVEL MEDIUM
> &END GLOBAL
> &FORCE_EVAL
> METHOD Quickstep
> &PRINT
> &FORCES OFF
> &END FORCES
> &END PRINT
> &DFT
> BASIS_SET_FILE_NAME /sp6/userexternal/vbellini/cp2k/BASIS/BASIS_MOLOPT
> POTENTIAL_FILE_NAME
> /sp6/userexternal/vbellini/cp2k/POTENTIAL/GTH_POTENTIALS
> RESTART_FILE_NAME ./working-RESTART.wfn
> LSD T
> MULTIPLICITY 24
> &MGRID
> CUTOFF 250
> NGRIDS 5
> &END MGRID
> &QS
> EXTRAPOLATION PS
> EXTRAPOLATION_ORDER 3
> &END QS
> &SCF
> SCF_GUESS restart
> EPS_SCF 5.0E-7
> MAX_SCF 50
> &OUTER_SCF ON
> MAX_SCF 20
> EPS_SCF 5.0E-7
> &END OUTER_SCF
> &OT ON
> N_DIIS 7
> MINIMIZER CG
> &END OT
> &PRINT
> &RESTART
> &EACH
> QS_SCF 10
> &END EACH
> ADD_LAST NUMERIC
> &END RESTART
> &END PRINT
> &END SCF
> &XC
> &VDW_POTENTIAL
> POTENTIAL_TYPE PAIR_POTENTIAL
> &PAIR_POTENTIAL
> REFERENCE_FUNCTIONAL PBE
> TYPE DFTD3
> PARAMETER_FILE_NAME /sp6/userexternal/vbellini/cp2k/dftd3.dat
> &END PAIR_POTENTIAL
> &END VDW_POTENTIAL
> &XC_FUNCTIONAL
> &PBE
> &END PBE
> &END XC_FUNCTIONAL
> &XC_GRID
> &END XC_GRID
> &END XC
> &END DFT
> &SUBSYS
> &CELL
> PERIODIC XY
> ABC 25.965 24.98484 45.0
> &END CELL
> &COORD
> @INCLUDE 'working.xyz'
> &END COORD
> &KIND Cr
> POTENTIAL GTH-PBE-q14
> BASIS_SET DZVP-MOLOPT-SR-GTH
> &BS OFF
> &ALPHA
> NEL -1 0
> L 0 2
> N 4 3
> &END
> &BETA
> NEL -1 -5
> L 0 2
> N 4 3
> &END
> &END BS
> &END KIND
> &KIND Ni
> POTENTIAL GTH-PBE-q18
> BASIS_SET DZVP-MOLOPT-SR-GTH
> &BS OFF
> &ALPHA
> NEL -1 0
> L 0 2
> N 4 3
> &END
> &BETA
> NEL -1 -5
> L 0 2
> N 4 3
> &END
> &END BS
> &END KIND
> &KIND F
> POTENTIAL GTH-PBE-q7
> BASIS_SET DZVP-MOLOPT-SR-GTH
> &END KIND
> &KIND O
> POTENTIAL GTH-PBE-q6
> BASIS_SET DZVP-MOLOPT-SR-GTH
> &END KIND
> &KIND C
> POTENTIAL GTH-PBE-q4
> BASIS_SET DZVP-MOLOPT-SR-GTH
> &END KIND
> &KIND N
> POTENTIAL GTH-PBE-q5
> BASIS_SET DZVP-MOLOPT-SR-GTH
> &END KIND
> &KIND H
> POTENTIAL GTH-PBE-q1
> BASIS_SET DZVP-MOLOPT-SR-GTH
> &END KIND
> &KIND S
> POTENTIAL GTH-PBE-q6
> BASIS_SET DZVP-MOLOPT-SR-GTH
> &END
> &KIND Au
> POTENTIAL GTH-PBE-q11
> BASIS_SET DZVP-MOLOPT-SR-GTH
> &END
> &END SUBSYS
> &END FORCE_EVAL
> &MOTION
> &GEO_OPT
> MAX_FORCE 0.0004
> MAX_ITER 500
> OPTIMIZER BFGS
> TYPE MINIMIZATION
> &END GEO_OPT
> &CONSTRAINT
> &CONSTRAINT_INFO
> &END CONSTRAINT_INFO
> &FIXED_ATOMS
> 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113
> 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
> 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215
> 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
> &END FIXED_ATOMS
> &END CONSTRAINT
> &END MOTION
>
>
> since I want to fix the first 270 atoms.
> I run the code, and the first restart input file, after the first
> minimization step, looks OK except that the fixed atoms list is truncated,
>
> &FIXED_ATOMS
> 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
> 100 101 102 103 \
> 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 15
> &END FIXED_ATOMS
>
> where the index 150 is also truncated to 15.
> Obviously during the minimization only the first 149 atoms are kept fixed.
> I tried to keep fixed other positions (e.g. from 91 to 260) and a similar
> problem occur, but truncation happens for a different atom index).
> It seems to me that there is a bug in that version of the code (previously
> I was running the version 2.1.160, and I never encountered such a problem)
> Did you find by chance an error in routines relevant to the above issue
> after the 30th of November in the source code, and corrected it?
> In order to update the code to the latest version I have to contact the
> local technician that is in charge to compile the code, since it is
> running in a machine located in a supercomputing center, so I wanted to be
> sure that
> the problem is relative only to the version downlodable at that date.
> Thanks for the help,
> cheers!
> Valerio
>
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