Commit 09b52a74 authored by Markus Scheidgen's avatar Markus Scheidgen
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Adapted to nomad-fair.

parent 0865874d
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Copyright 2017 Berk Onat
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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/*
* Copyright 2017-2018 Berk Onat, Fawzi Mohamed
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package eu.nomad_lab.parsers
import eu.nomad_lab
import eu.nomad_lab.DefaultPythonInterpreter
import org.{ json4s => jn }
import eu.{ nomad_lab => lab }
import scala.collection.breakOut
object AmberParser extends SimpleExternalParserGenerator(
name = "AmberParser",
parserInfo = jn.JObject(
("name" -> jn.JString("AmberParser")) ::
("parserId" -> jn.JString("AmberParser" + lab.AmberVersionInfo.version)) ::
("versionInfo" -> jn.JObject(
("nomadCoreVersion" -> jn.JObject(lab.NomadCoreVersionInfo.toMap.map {
case (k, v) => k -> jn.JString(v.toString)
}(breakOut): List[(String, jn.JString)])) ::
(lab.AmberVersionInfo.toMap.map {
case (key, value) =>
(key -> jn.JString(value.toString))
}(breakOut): List[(String, jn.JString)])
)) :: Nil
),
mainFileTypes = Seq("text/.*"),
mainFileRe = """\s*Amber\s*[0-9]+""".r,
cmd = Seq(DefaultPythonInterpreter.pythonExe(), "${envDir}/parsers/amber/parser/parser-amber/AMBERParser.py",
"${mainFilePath}"),
resList = Seq(
"parser-amber/AMBERParser.py",
"parser-amber/AMBERDictionary.py",
"parser-amber/AMBERCommon.py",
"parser-amber/MetaInfoStorage.py",
"parser-amber/trajectory_reader.py",
"parser-amber/setup_paths.py",
"nomad_meta_info/public.nomadmetainfo.json",
"nomad_meta_info/common.nomadmetainfo.json",
"nomad_meta_info/meta_types.nomadmetainfo.json",
"nomad_meta_info/amber.nomadmetainfo.json"
) ++ DefaultPythonInterpreter.commonFiles(),
dirMap = Map(
"parser-amber" -> "parsers/amber/parser/parser-amber",
"nomad_meta_info" -> "nomad-meta-info/meta_info/nomad_meta_info",
"python" -> "python-common/common/python/nomadcore"
) ++ DefaultPythonInterpreter.commonDirMapping(),
metaInfoEnv = Some(lab.meta.KnownMetaInfoEnvs.amber)
)
/*
* Copyright 2017-2018 Berk Onat, Fawzi Mohamed
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package eu.nomad_lab.parsers
import org.specs2.mutable.Specification
object AmberParserSpec extends Specification {
"AmberParserTest" >> {
"test with json-events" >> {
ParserRun.parse(AmberParser, "parsers/amber/test/examples/03_Prod.out", "json-events") must_== ParseResult.ParseSuccess
}
"test with json" >> {
ParserRun.parse(AmberParser, "parsers/amber/test/examples/03_Prod.out", "json") must_== ParseResult.ParseSuccess
}
}
}
-------------------------------------------------------
Amber 16 SANDER 2016
-------------------------------------------------------
| Run on 05/17/2017 at 23:45:51
| Executable path: ../bin/sander
| Working directory: /Users/bonat/AMBER/amber16/Tutorial
| Hostname: Unknown
[-O]verwriting output
File Assignments:
| MDIN: 01_Min.in
| MDOUT: 01_Min.out
|INPCRD: inpcrd
| PARM: prmtop
|RESTRT: 01_Min.rst
| REFC: refc
| MDVEL: mdvel
| MDFRC: mdfrc
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: 01_Min.mdinfo
| MTMD: mtmd
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: inptraj
Here is the input file:
Minimize
&cntrl
imin=1,
ntx=1,
irest=0,
maxcyc=2000,
ncyc=1000,
ntpr=100,
ntwx=0,
cut=8.0,
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read
| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 14.636
| New format PARM file being parsed.
| Version = 1.000 Date = 06/30/15 Time = 11:44:23
NATOM = 1912 NTYPES = 9 NBONH = 1902 MBONA = 9
NTHETH = 25 MTHETA = 11 NPHIH = 43 MPHIA = 24
NHPARM = 0 NPARM = 0 NNB = 2619 NRES = 633
NBONA = 9 NTHETA = 11 NPHIA = 24 NUMBND = 13
NUMANG = 21 NPTRA = 20 NATYP = 10 NPHB = 1
IFBOX = 1 NMXRS = 10 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 236620
| Hollerith 6371
| Integer 66720
| Max Pairs 637333
| nblistReal 22944
| nblist Int 109618
| Total 5231 kbytes
| Note: 1-4 EEL scale factors are being read from the topology file.
| Note: 1-4 VDW scale factors are being read from the topology file.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
ACE
General flags:
imin = 1, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 2, ntpr = 100, ntrx = 1, ntwr = 1
iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0
ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 1, ntb = 1, igb = 0, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 8.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Energy minimization:
maxcyc = 2000, ncyc = 1000, ntmin = 1
dx0 = 0.01000, drms = 0.00010
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
vdwmeth = 1, eedmeth = 1, netfrc = 0
Box X = 31.398 Box Y = 34.100 Box Z = 29.273
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 32 NFFT2 = 36 NFFT3 = 30
Cutoff= 8.000 Tol =0.100E-04
Ewald Coefficient = 0.34864
Interpolation order = 4
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
ACE
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 630
Sum of charges from parm topology file = -0.00000000
Forcing neutrality...
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 263495
| TOTAL SIZE OF NONBOND LIST = 263495
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -4.8111E+03 1.1635E+01 4.4016E+01 O 1544
BOND = 0.0510 ANGLE = 0.3620 DIHED = 9.6440
VDWAALS = 627.5975 EEL = -5502.6684 HBOND = 0.0000
1-4 VDW = 5.0157 1-4 EEL = 48.9355 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
100 -6.1212E+03 1.4891E+00 5.2970E+00 H1 1251
BOND = 342.6762 ANGLE = 1.0090 DIHED = 9.2581
VDWAALS = 743.6353 EEL = -7267.5869 HBOND = 0.0000
1-4 VDW = 3.0776 1-4 EEL = 46.7355 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
200 -6.3600E+03 1.9636E+00 8.8730E+00 H1 207
BOND = 426.2999 ANGLE = 0.9976 DIHED = 9.0480
VDWAALS = 869.3107 EEL = -7715.4488 HBOND = 0.0000
1-4 VDW = 3.0020 1-4 EEL = 46.7519 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
300 -6.5061E+03 1.6982E+00 9.0567E+00 H2 619
BOND = 394.1819 ANGLE = 0.9374 DIHED = 8.9559
VDWAALS = 964.5110 EEL = -7924.4005 HBOND = 0.0000
1-4 VDW = 2.9656 1-4 EEL = 46.7381 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
400 -6.6119E+03 1.4562E+00 8.4384E+00 H1 687
BOND = 457.7683 ANGLE = 0.9340 DIHED = 8.9064
VDWAALS = 1039.4566 EEL = -8168.5759 HBOND = 0.0000
1-4 VDW = 2.9078 1-4 EEL = 46.7069 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
500 -6.6944E+03 1.2313E+00 8.0503E+00 H2 619
BOND = 431.3054 ANGLE = 0.9097 DIHED = 8.8762
VDWAALS = 1101.5528 EEL = -8286.5884 HBOND = 0.0000
1-4 VDW = 2.8770 1-4 EEL = 46.6522 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
600 -6.7604E+03 1.1079E+00 9.4867E+00 C 15
BOND = 476.1192 ANGLE = 0.9169 DIHED = 8.8552
VDWAALS = 1152.3699 EEL = -8448.1407 HBOND = 0.0000
1-4 VDW = 2.8272 1-4 EEL = 46.6332 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
700 -6.8166E+03 9.0444E-01 1.4664E+01 C 15
BOND = 457.4262 ANGLE = 0.9088 DIHED = 8.8410
VDWAALS = 1193.2976 EEL = -8526.4271 HBOND = 0.0000
1-4 VDW = 2.8257 1-4 EEL = 46.5586 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
800 -6.8668E+03 4.4732E-01 9.1305E+00 C 15
BOND = 479.5699 ANGLE = 0.9061 DIHED = 8.8278
VDWAALS = 1227.3444 EEL = -8632.7783 HBOND = 0.0000
1-4 VDW = 2.7849 1-4 EEL = 46.5480 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
900 -6.9124E+03 6.2985E-01 2.0555E+01 C 15
BOND = 480.2808 ANGLE = 0.9221 DIHED = 8.8190
VDWAALS = 1256.4214 EEL = -8708.0642 HBOND = 0.0000
1-4 VDW = 2.7970 1-4 EEL = 46.4537 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1000 -6.9547E+03 3.0897E-01 3.3644E+00 C 15
BOND = 489.4883 ANGLE = 0.9079 DIHED = 8.8097
VDWAALS = 1282.9419 EEL = -8786.0553 HBOND = 0.0000
1-4 VDW = 2.7684 1-4 EEL = 46.4290 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1100 -7.1662E+03 1.1988E+00 1.8363E+01 H 18
BOND = 532.3344 ANGLE = 1.4685 DIHED = 8.8329
VDWAALS = 1477.1170 EEL = -9235.4299 HBOND = 0.0000
1-4 VDW = 3.0533 1-4 EEL = 46.4327 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1200 -7.2356E+03 6.1721E-01 1.0182E+01 HB1 12
BOND = 544.3367 ANGLE = 1.1159 DIHED = 8.7529
VDWAALS = 1512.6509 EEL = -9351.9937 HBOND = 0.0000
1-4 VDW = 2.9892 1-4 EEL = 46.5304 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1300 -7.2838E+03 6.9171E-01 1.1999E+01 H 18
BOND = 553.0078 ANGLE = 1.1451 DIHED = 8.7505
VDWAALS = 1554.5594 EEL = -9450.7545 HBOND = 0.0000
1-4 VDW = 3.0288 1-4 EEL = 46.4202 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1400 -7.3353E+03 1.4209E+00 3.5845E+01 N 7
BOND = 571.6819 ANGLE = 1.7273 DIHED = 9.1142
VDWAALS = 1604.6538 EEL = -9571.6987 HBOND = 0.0000
1-4 VDW = 2.7844 1-4 EEL = 46.4782 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1500 -7.3845E+03 6.4967E-01 1.5487E+01 C 15
BOND = 574.7272 ANGLE = 1.2549 DIHED = 8.8178
VDWAALS = 1641.0953 EEL = -9659.7608 HBOND = 0.0000
1-4 VDW = 2.7656 1-4 EEL = 46.5803 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1600 -7.4140E+03 6.3566E-01 1.7181E+01 C 15
BOND = 581.3177 ANGLE = 1.0348 DIHED = 8.8171
VDWAALS = 1671.1224 EEL = -9725.4041 HBOND = 0.0000
1-4 VDW = 2.7264 1-4 EEL = 46.4242 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1700 -7.4411E+03 6.6989E-01 1.3341E+01 C 15
BOND = 587.2115 ANGLE = 0.9408 DIHED = 8.8389
VDWAALS = 1693.8494 EEL = -9780.8385 HBOND = 0.0000
1-4 VDW = 2.6734 1-4 EEL = 46.2351 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1800 -7.4669E+03 7.1067E-01 2.1048E+01 C 15
BOND = 592.2722 ANGLE = 0.9321 DIHED = 8.8075
VDWAALS = 1721.0583 EEL = -9838.6788 HBOND = 0.0000
1-4 VDW = 2.6862 1-4 EEL = 46.0228 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1900 -7.4907E+03 4.6866E-01 1.0809E+01 C 15
BOND = 596.5214 ANGLE = 0.7892 DIHED = 8.7554
VDWAALS = 1744.1146 EEL = -9889.6934 HBOND = 0.0000
1-4 VDW = 2.6840 1-4 EEL = 46.0804 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
2000 -7.5136E+03 6.8267E-01 1.7223E+01 C 15
BOND = 602.5153 ANGLE = 1.1086 DIHED = 8.7394
VDWAALS = 1757.1386 EEL = -9931.8105 HBOND = 0.0000
1-4 VDW = 2.6428 1-4 EEL = 46.0732 RESTRAINT = 0.0000
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
2000 -7.5136E+03 6.8267E-01 1.7223E+01 C 15
BOND = 602.5153 ANGLE = 1.1086 DIHED = 8.7394
VDWAALS = 1757.1386 EEL = -9931.8105 HBOND = 0.0000
1-4 VDW = 2.6428 1-4 EEL = 46.0732 RESTRAINT = 0.0000
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| Build the list 0.08 (83.57% of List )
| Other 0.02 (16.43% of List )
| List time 0.09 ( 0.61% of Nonbo)
| Short_ene time 10.94 (99.07% of Direc)
| Other 0.10 ( 0.93% of Direc)
| Direct Ewald time 11.04 (72.20% of Ewald)
| Adjust Ewald time 0.12 ( 0.79% of Ewald)
| Self Ewald time 0.00 ( 0.01% of Ewald)
| Fill Bspline coeffs 0.13 ( 3.12% of Recip)
| Fill charge grid 0.42 (10.27% of Recip)