Commit 28e0623a authored by Silvia Chiacchiera's avatar Silvia Chiacchiera

.gitinore line changed to be as in master

parents d4cb4c00 4190ac57
......@@ -2,6 +2,6 @@ _build
_templates
_static
*.pyc
#*
*#
*~
general.txt
......@@ -10,4 +10,4 @@ pages:
paths:
- public
only:
- master
- adjustments
......@@ -61,7 +61,7 @@ The following modules connected to the DL_MESO_DPD code have been produce so far
./modules/DL_MESO_DPD/dipole_dlmeso_dpd/readme
./modules/DL_MESO_DPD/format_dlmeso_dpd/readme
./modules/DL_MESO_DPD/dipole_af_dlmeso_dpd/readme
ESDW Barcelona 2017
......
DL_MESO charged harmonic dimers with dpd repulsion
volume 64.0
temperature 1.0
cutoff 1.0
timestep 0.01
steps 70000
equilibration steps 20000
traj 20000 10
stats every 100
stack size 100
print every 100
job time 7200.0
close time 10.0
ensemble nvt mdvv
ewald sum 1.0 5 5 5
bjerrum 42.0
smear gauss equal
finish
DL_MESO charged harmonic dimers with dpd repulsion
5001 100
DIMER
0.000000E+00 1.500096E+01 1.000000E+00
1.000000E-01 1.443052E+01 9.619731E-01
2.000000E-01 1.301975E+01 8.679278E-01
3.000000E-01 1.123656E+01 7.490557E-01
4.000000E-01 9.404209E+00 6.269071E-01
5.000000E-01 7.679286E+00 5.119196E-01
6.000000E-01 6.134042E+00 4.089099E-01
7.000000E-01 4.803145E+00 3.201892E-01
8.000000E-01 3.692590E+00 2.461569E-01
9.000000E-01 2.781081E+00 1.853935E-01
1.000000E+00 2.025838E+00 1.350472E-01
1.100000E+00 1.391383E+00 9.275290E-02
1.200000E+00 8.680427E-01 5.786580E-02
1.300000E+00 4.584099E-01 3.055870E-02
1.400000E+00 1.600278E-01 1.066784E-02
1.500000E+00 -4.321282E-02 -2.880670E-03
1.600000E+00 -1.754114E-01 -1.169334E-02
1.700000E+00 -2.601105E-01 -1.733959E-02
1.800000E+00 -3.140534E-01 -2.093555E-02
1.900000E+00 -3.438671E-01 -2.292300E-02
2.000000E+00 -3.520069E-01 -2.346562E-02
2.100000E+00 -3.450019E-01 -2.299865E-02
2.200000E+00 -3.327794E-01 -2.218387E-02
2.300000E+00 -3.203573E-01 -2.135578E-02
2.400000E+00 -3.030559E-01 -2.020243E-02
2.500000E+00 -2.725846E-01 -1.817114E-02
2.600000E+00 -2.238979E-01 -1.492557E-02
2.700000E+00 -1.548837E-01 -1.032492E-02
2.800000E+00 -6.861446E-02 -4.574004E-03
2.900000E+00 2.620253E-02 1.746723E-03
3.000000E+00 1.160390E-01 7.735436E-03
3.100000E+00 1.880601E-01 1.253653E-02
3.200000E+00 2.327281E-01 1.551422E-02
3.300000E+00 2.444153E-01 1.629331E-02
3.400000E+00 2.204886E-01 1.469830E-02
3.500000E+00 1.651585E-01 1.100986E-02
3.600000E+00 8.861101E-02 5.907022E-03
3.700000E+00 7.173339E-03 4.781919E-04
3.800000E+00 -6.240342E-02 -4.159962E-03
3.900000E+00 -1.082654E-01 -7.217229E-03
4.000000E+00 -1.274511E-01 -8.496194E-03
4.100000E+00 -1.194502E-01 -7.962834E-03
4.200000E+00 -8.297840E-02 -5.531539E-03
4.300000E+00 -2.353598E-02 -1.568965E-03
4.400000E+00 4.931168E-02 3.287235E-03
4.500000E+00 1.243524E-01 8.289630E-03
4.600000E+00 1.946555E-01 1.297620E-02
4.700000E+00 2.579271E-01 1.719404E-02
4.800000E+00 3.144807E-01 2.096404E-02
4.900000E+00 3.652996E-01 2.435175E-02
5.000000E+00 4.090729E-01 2.726978E-02
5.100000E+00 4.463736E-01 2.975633E-02
5.200000E+00 4.815185E-01 3.209918E-02
5.300000E+00 5.216901E-01 3.477711E-02
5.400000E+00 5.722338E-01 3.814647E-02
5.500000E+00 6.269027E-01 4.179083E-02
5.600000E+00 6.753958E-01 4.502350E-02
5.700000E+00 7.124729E-01 4.749515E-02
5.800000E+00 7.340793E-01 4.893548E-02
5.900000E+00 7.350656E-01 4.900123E-02
6.000000E+00 7.098858E-01 4.732268E-02
6.100000E+00 6.510291E-01 4.339916E-02
6.200000E+00 5.532835E-01 3.688321E-02
6.300000E+00 4.182946E-01 2.788452E-02
6.400000E+00 2.506792E-01 1.671088E-02
6.500000E+00 6.239041E-02 4.159094E-03
6.600000E+00 -1.270109E-01 -8.466848E-03
6.700000E+00 -2.973823E-01 -1.982422E-02
6.800000E+00 -4.344376E-01 -2.896065E-02
6.900000E+00 -5.315588E-01 -3.543498E-02
7.000000E+00 -5.882560E-01 -3.921455E-02
7.100000E+00 -6.089954E-01 -4.059709E-02
7.200000E+00 -6.046352E-01 -4.030643E-02
7.300000E+00 -5.913784E-01 -3.942270E-02
7.400000E+00 -5.802981E-01 -3.868406E-02
7.500000E+00 -5.769458E-01 -3.846059E-02
7.600000E+00 -5.765742E-01 -3.843582E-02
7.700000E+00 -5.712677E-01 -3.808207E-02
7.800000E+00 -5.557976E-01 -3.705080E-02
7.900000E+00 -5.232541E-01 -3.488137E-02
8.000000E+00 -4.652353E-01 -3.101370E-02
8.100000E+00 -3.803252E-01 -2.535339E-02
8.200000E+00 -2.763238E-01 -1.842040E-02
8.300000E+00 -1.617412E-01 -1.078206E-02
8.400000E+00 -4.099145E-02 -2.732588E-03
8.500000E+00 8.007282E-02 5.337846E-03
8.600000E+00 1.889391E-01 1.259514E-02
8.700000E+00 2.704650E-01 1.802985E-02
8.800000E+00 3.128353E-01 2.085435E-02
8.900000E+00 3.131113E-01 2.087275E-02
9.000000E+00 2.772904E-01 1.848484E-02
9.100000E+00 2.135328E-01 1.423461E-02
9.200000E+00 1.312026E-01 8.746283E-03
9.300000E+00 4.391893E-02 2.927741E-03
9.400000E+00 -2.845610E-02 -1.896952E-03
9.500000E+00 -6.899722E-02 -4.599520E-03
9.600000E+00 -6.921033E-02 -4.613726E-03
9.700000E+00 -3.118518E-02 -2.078879E-03
9.800000E+00 3.666647E-02 2.444275E-03
9.900000E+00 1.257607E-01 8.383507E-03
all species
0.000000E+00 1.500096E+01 1.000000E+00
1.000000E-01 1.443052E+01 9.619731E-01
2.000000E-01 1.301975E+01 8.679278E-01
3.000000E-01 1.123656E+01 7.490557E-01
4.000000E-01 9.404209E+00 6.269071E-01
5.000000E-01 7.679286E+00 5.119196E-01
6.000000E-01 6.134042E+00 4.089099E-01
7.000000E-01 4.803145E+00 3.201892E-01
8.000000E-01 3.692590E+00 2.461569E-01
9.000000E-01 2.781081E+00 1.853935E-01
1.000000E+00 2.025838E+00 1.350472E-01
1.100000E+00 1.391383E+00 9.275290E-02
1.200000E+00 8.680427E-01 5.786580E-02
1.300000E+00 4.584099E-01 3.055870E-02
1.400000E+00 1.600278E-01 1.066784E-02
1.500000E+00 -4.321282E-02 -2.880670E-03
1.600000E+00 -1.754114E-01 -1.169334E-02
1.700000E+00 -2.601105E-01 -1.733959E-02
1.800000E+00 -3.140534E-01 -2.093555E-02
1.900000E+00 -3.438671E-01 -2.292300E-02
2.000000E+00 -3.520069E-01 -2.346562E-02
2.100000E+00 -3.450019E-01 -2.299865E-02
2.200000E+00 -3.327794E-01 -2.218387E-02
2.300000E+00 -3.203573E-01 -2.135578E-02
2.400000E+00 -3.030559E-01 -2.020243E-02
2.500000E+00 -2.725846E-01 -1.817114E-02
2.600000E+00 -2.238979E-01 -1.492557E-02
2.700000E+00 -1.548837E-01 -1.032492E-02
2.800000E+00 -6.861446E-02 -4.574004E-03
2.900000E+00 2.620253E-02 1.746723E-03
3.000000E+00 1.160390E-01 7.735436E-03
3.100000E+00 1.880601E-01 1.253653E-02
3.200000E+00 2.327281E-01 1.551422E-02
3.300000E+00 2.444153E-01 1.629331E-02
3.400000E+00 2.204886E-01 1.469830E-02
3.500000E+00 1.651585E-01 1.100986E-02
3.600000E+00 8.861101E-02 5.907022E-03
3.700000E+00 7.173339E-03 4.781919E-04
3.800000E+00 -6.240342E-02 -4.159962E-03
3.900000E+00 -1.082654E-01 -7.217229E-03
4.000000E+00 -1.274511E-01 -8.496194E-03
4.100000E+00 -1.194502E-01 -7.962834E-03
4.200000E+00 -8.297840E-02 -5.531539E-03
4.300000E+00 -2.353598E-02 -1.568965E-03
4.400000E+00 4.931168E-02 3.287235E-03
4.500000E+00 1.243524E-01 8.289630E-03
4.600000E+00 1.946555E-01 1.297620E-02
4.700000E+00 2.579271E-01 1.719404E-02
4.800000E+00 3.144807E-01 2.096404E-02
4.900000E+00 3.652996E-01 2.435175E-02
5.000000E+00 4.090729E-01 2.726978E-02
5.100000E+00 4.463736E-01 2.975633E-02
5.200000E+00 4.815185E-01 3.209918E-02
5.300000E+00 5.216901E-01 3.477711E-02
5.400000E+00 5.722338E-01 3.814647E-02
5.500000E+00 6.269027E-01 4.179083E-02
5.600000E+00 6.753958E-01 4.502350E-02
5.700000E+00 7.124729E-01 4.749515E-02
5.800000E+00 7.340793E-01 4.893548E-02
5.900000E+00 7.350656E-01 4.900123E-02
6.000000E+00 7.098858E-01 4.732268E-02
6.100000E+00 6.510291E-01 4.339916E-02
6.200000E+00 5.532835E-01 3.688321E-02
6.300000E+00 4.182946E-01 2.788452E-02
6.400000E+00 2.506792E-01 1.671088E-02
6.500000E+00 6.239041E-02 4.159094E-03
6.600000E+00 -1.270109E-01 -8.466848E-03
6.700000E+00 -2.973823E-01 -1.982422E-02
6.800000E+00 -4.344376E-01 -2.896065E-02
6.900000E+00 -5.315588E-01 -3.543498E-02
7.000000E+00 -5.882560E-01 -3.921455E-02
7.100000E+00 -6.089954E-01 -4.059709E-02
7.200000E+00 -6.046352E-01 -4.030643E-02
7.300000E+00 -5.913784E-01 -3.942270E-02
7.400000E+00 -5.802981E-01 -3.868406E-02
7.500000E+00 -5.769458E-01 -3.846059E-02
7.600000E+00 -5.765742E-01 -3.843582E-02
7.700000E+00 -5.712677E-01 -3.808207E-02
7.800000E+00 -5.557976E-01 -3.705080E-02
7.900000E+00 -5.232541E-01 -3.488137E-02
8.000000E+00 -4.652353E-01 -3.101370E-02
8.100000E+00 -3.803252E-01 -2.535339E-02
8.200000E+00 -2.763238E-01 -1.842040E-02
8.300000E+00 -1.617412E-01 -1.078206E-02
8.400000E+00 -4.099145E-02 -2.732588E-03
8.500000E+00 8.007282E-02 5.337846E-03
8.600000E+00 1.889391E-01 1.259514E-02
8.700000E+00 2.704650E-01 1.802985E-02
8.800000E+00 3.128353E-01 2.085435E-02
8.900000E+00 3.131113E-01 2.087275E-02
9.000000E+00 2.772904E-01 1.848484E-02
9.100000E+00 2.135328E-01 1.423461E-02
9.200000E+00 1.312026E-01 8.746283E-03
9.300000E+00 4.391893E-02 2.927741E-03
9.400000E+00 -2.845610E-02 -1.896952E-03
9.500000E+00 -6.899722E-02 -4.599520E-03
9.600000E+00 -6.921033E-02 -4.613726E-03
9.700000E+00 -3.118518E-02 -2.078879E-03
9.800000E+00 3.666647E-02 2.444275E-03
9.900000E+00 1.257607E-01 8.383507E-03
DL_MESO charged harmonic dimers with dpd repulsion
5001 100
DIMER
0.000000E+00 6.233649E+00 0.000000E+00
6.283185E-01 5.405816E+00 -1.412683E+00
1.256637E+00 6.257941E+00 -2.520388E+00
1.884956E+00 4.150463E+00 -2.387533E+00
2.513274E+00 2.693334E+00 -3.912521E+00
3.141593E+00 2.131104E+00 -3.246574E+00
3.769911E+00 1.650412E+00 -2.860556E+00
4.398230E+00 1.278705E+00 -2.801992E+00
5.026548E+00 1.124330E+00 -2.102817E+00
5.654867E+00 9.385175E-01 -1.890993E+00
6.283185E+00 7.935981E-01 -1.756010E+00
6.911504E+00 7.270662E-01 -1.552284E+00
7.539822E+00 6.561622E-01 -1.394604E+00
8.168141E+00 6.057526E-01 -1.279770E+00
8.796459E+00 5.775685E-01 -1.163291E+00
9.424778E+00 5.520783E-01 -1.061300E+00
1.005310E+01 5.454682E-01 -9.692359E-01
1.068142E+01 5.360120E-01 -8.920519E-01
1.130973E+01 5.334286E-01 -8.332761E-01
1.193805E+01 5.220814E-01 -7.755050E-01
1.256637E+01 5.183182E-01 -7.251774E-01
1.319469E+01 5.112317E-01 -6.779455E-01
1.382301E+01 5.105991E-01 -6.323132E-01
1.445133E+01 5.072763E-01 -5.897462E-01
1.507964E+01 5.032710E-01 -5.526064E-01
1.570796E+01 5.016128E-01 -5.167255E-01
1.633628E+01 5.003218E-01 -4.838756E-01
1.696460E+01 4.998379E-01 -4.524754E-01
1.759292E+01 4.990584E-01 -4.239900E-01
1.822124E+01 4.978744E-01 -3.965512E-01
1.884956E+01 4.972975E-01 -3.710976E-01
1.947787E+01 4.971236E-01 -3.465874E-01
2.010619E+01 4.964664E-01 -3.229971E-01
2.073451E+01 4.963465E-01 -3.006642E-01
2.136283E+01 4.957162E-01 -2.790428E-01
2.199115E+01 4.956949E-01 -2.584603E-01
2.261947E+01 4.954903E-01 -2.382167E-01
2.324779E+01 4.951425E-01 -2.189718E-01
2.387610E+01 4.951592E-01 -2.001491E-01
2.450442E+01 4.950445E-01 -1.818502E-01
2.513274E+01 4.950193E-01 -1.639092E-01
2.576106E+01 4.948790E-01 -1.466196E-01
2.638938E+01 4.947980E-01 -1.294565E-01
2.701770E+01 4.948071E-01 -1.127194E-01
2.764602E+01 4.946385E-01 -9.609770E-02
2.827433E+01 4.946320E-01 -7.983630E-02
2.890265E+01 4.946369E-01 -6.370879E-02
2.953097E+01 4.945749E-01 -4.756847E-02
3.015929E+01 4.945944E-01 -3.168217E-02
3.078761E+01 4.945815E-01 -1.587042E-02
3.141593E+01 4.945837E-01 0.000000E+00
3.204425E+01 4.945815E-01 1.587042E-02
3.267256E+01 4.945944E-01 3.168217E-02
3.330088E+01 4.945749E-01 4.756847E-02
3.392920E+01 4.946369E-01 6.370879E-02
3.455752E+01 4.946320E-01 7.983630E-02
3.518584E+01 4.946385E-01 9.609770E-02
3.581416E+01 4.948071E-01 1.127194E-01
3.644247E+01 4.947980E-01 1.294565E-01
3.707079E+01 4.948790E-01 1.466196E-01
3.769911E+01 4.950193E-01 1.639092E-01
3.832743E+01 4.950445E-01 1.818502E-01
3.895575E+01 4.951592E-01 2.001491E-01
3.958407E+01 4.951425E-01 2.189718E-01
4.021239E+01 4.954903E-01 2.382167E-01
4.084070E+01 4.956949E-01 2.584603E-01
4.146902E+01 4.957162E-01 2.790428E-01
4.209734E+01 4.963465E-01 3.006642E-01
4.272566E+01 4.964664E-01 3.229971E-01
4.335398E+01 4.971236E-01 3.465874E-01
4.398230E+01 4.972975E-01 3.710976E-01
4.461062E+01 4.978744E-01 3.965512E-01
4.523893E+01 4.990584E-01 4.239900E-01
4.586725E+01 4.998379E-01 4.524754E-01
4.649557E+01 5.003218E-01 4.838756E-01
4.712389E+01 5.016128E-01 5.167255E-01
4.775221E+01 5.032710E-01 5.526064E-01
4.838053E+01 5.072763E-01 5.897462E-01
4.900885E+01 5.105991E-01 6.323132E-01
4.963716E+01 5.112317E-01 6.779455E-01
5.026548E+01 5.183182E-01 7.251774E-01
5.089380E+01 5.220814E-01 7.755050E-01
5.152212E+01 5.334286E-01 8.332761E-01
5.215044E+01 5.360120E-01 8.920519E-01
5.277876E+01 5.454682E-01 9.692359E-01
5.340708E+01 5.520783E-01 1.061300E+00
5.403539E+01 5.775685E-01 1.163291E+00
5.466371E+01 6.057526E-01 1.279770E+00
5.529203E+01 6.561622E-01 1.394604E+00
5.592035E+01 7.270662E-01 1.552284E+00
5.654867E+01 7.935981E-01 1.756010E+00
5.717699E+01 9.385175E-01 1.890993E+00
5.780530E+01 1.124330E+00 2.102817E+00
5.843362E+01 1.278705E+00 2.801992E+00
5.906194E+01 1.650412E+00 2.860556E+00
5.969026E+01 2.131104E+00 3.246574E+00
6.031858E+01 2.693334E+00 3.912521E+00
6.094690E+01 4.150463E+00 2.387533E+00
6.157522E+01 6.257941E+00 2.520388E+00
6.220353E+01 5.405816E+00 1.412683E+00
all species
0.000000E+00 6.233649E+00 0.000000E+00
6.283185E-01 5.405816E+00 -1.412683E+00
1.256637E+00 6.257941E+00 -2.520388E+00
1.884956E+00 4.150463E+00 -2.387533E+00
2.513274E+00 2.693334E+00 -3.912521E+00
3.141593E+00 2.131104E+00 -3.246574E+00
3.769911E+00 1.650412E+00 -2.860556E+00
4.398230E+00 1.278705E+00 -2.801992E+00
5.026548E+00 1.124330E+00 -2.102817E+00
5.654867E+00 9.385175E-01 -1.890993E+00
6.283185E+00 7.935981E-01 -1.756010E+00
6.911504E+00 7.270662E-01 -1.552284E+00
7.539822E+00 6.561622E-01 -1.394604E+00
8.168141E+00 6.057526E-01 -1.279770E+00
8.796459E+00 5.775685E-01 -1.163291E+00
9.424778E+00 5.520783E-01 -1.061300E+00
1.005310E+01 5.454682E-01 -9.692359E-01
1.068142E+01 5.360120E-01 -8.920519E-01
1.130973E+01 5.334286E-01 -8.332761E-01
1.193805E+01 5.220814E-01 -7.755050E-01
1.256637E+01 5.183182E-01 -7.251774E-01
1.319469E+01 5.112317E-01 -6.779455E-01
1.382301E+01 5.105991E-01 -6.323132E-01
1.445133E+01 5.072763E-01 -5.897462E-01
1.507964E+01 5.032710E-01 -5.526064E-01
1.570796E+01 5.016128E-01 -5.167255E-01
1.633628E+01 5.003218E-01 -4.838756E-01
1.696460E+01 4.998379E-01 -4.524754E-01
1.759292E+01 4.990584E-01 -4.239900E-01
1.822124E+01 4.978744E-01 -3.965512E-01
1.884956E+01 4.972975E-01 -3.710976E-01
1.947787E+01 4.971236E-01 -3.465874E-01
2.010619E+01 4.964664E-01 -3.229971E-01
2.073451E+01 4.963465E-01 -3.006642E-01
2.136283E+01 4.957162E-01 -2.790428E-01
2.199115E+01 4.956949E-01 -2.584603E-01
2.261947E+01 4.954903E-01 -2.382167E-01
2.324779E+01 4.951425E-01 -2.189718E-01
2.387610E+01 4.951592E-01 -2.001491E-01
2.450442E+01 4.950445E-01 -1.818502E-01
2.513274E+01 4.950193E-01 -1.639092E-01
2.576106E+01 4.948790E-01 -1.466196E-01
2.638938E+01 4.947980E-01 -1.294565E-01
2.701770E+01 4.948071E-01 -1.127194E-01
2.764602E+01 4.946385E-01 -9.609770E-02
2.827433E+01 4.946320E-01 -7.983630E-02
2.890265E+01 4.946369E-01 -6.370879E-02
2.953097E+01 4.945749E-01 -4.756847E-02
3.015929E+01 4.945944E-01 -3.168217E-02
3.078761E+01 4.945815E-01 -1.587042E-02
3.141593E+01 4.945837E-01 0.000000E+00
3.204425E+01 4.945815E-01 1.587042E-02
3.267256E+01 4.945944E-01 3.168217E-02
3.330088E+01 4.945749E-01 4.756847E-02
3.392920E+01 4.946369E-01 6.370879E-02
3.455752E+01 4.946320E-01 7.983630E-02
3.518584E+01 4.946385E-01 9.609770E-02
3.581416E+01 4.948071E-01 1.127194E-01
3.644247E+01 4.947980E-01 1.294565E-01
3.707079E+01 4.948790E-01 1.466196E-01
3.769911E+01 4.950193E-01 1.639092E-01
3.832743E+01 4.950445E-01 1.818502E-01
3.895575E+01 4.951592E-01 2.001491E-01
3.958407E+01 4.951425E-01 2.189718E-01
4.021239E+01 4.954903E-01 2.382167E-01
4.084070E+01 4.956949E-01 2.584603E-01
4.146902E+01 4.957162E-01 2.790428E-01
4.209734E+01 4.963465E-01 3.006642E-01
4.272566E+01 4.964664E-01 3.229971E-01
4.335398E+01 4.971236E-01 3.465874E-01
4.398230E+01 4.972975E-01 3.710976E-01
4.461062E+01 4.978744E-01 3.965512E-01
4.523893E+01 4.990584E-01 4.239900E-01
4.586725E+01 4.998379E-01 4.524754E-01
4.649557E+01 5.003218E-01 4.838756E-01
4.712389E+01 5.016128E-01 5.167255E-01
4.775221E+01 5.032710E-01 5.526064E-01
4.838053E+01 5.072763E-01 5.897462E-01
4.900885E+01 5.105991E-01 6.323132E-01
4.963716E+01 5.112317E-01 6.779455E-01
5.026548E+01 5.183182E-01 7.251774E-01
5.089380E+01 5.220814E-01 7.755050E-01
5.152212E+01 5.334286E-01 8.332761E-01
5.215044E+01 5.360120E-01 8.920519E-01
5.277876E+01 5.454682E-01 9.692359E-01
5.340708E+01 5.520783E-01 1.061300E+00
5.403539E+01 5.775685E-01 1.163291E+00
5.466371E+01 6.057526E-01 1.279770E+00
5.529203E+01 6.561622E-01 1.394604E+00
5.592035E+01 7.270662E-01 1.552284E+00
5.654867E+01 7.935981E-01 1.756010E+00
5.717699E+01 9.385175E-01 1.890993E+00
5.780530E+01 1.124330E+00 2.102817E+00
5.843362E+01 1.278705E+00 2.801992E+00
5.906194E+01 1.650412E+00 2.860556E+00
5.969026E+01 2.131104E+00 3.246574E+00
6.031858E+01 2.693334E+00 3.912521E+00
6.094690E+01 4.150463E+00 2.387533E+00
6.157522E+01 6.257941E+00 2.520388E+00
6.220353E+01 5.405816E+00 1.412683E+00
DL_MESO charged harmonic dimers with dpd repulsion
SPECIES 2
solp 1.0 0.46 0
solm 1.0 -0.46 0
MOLECULES 1
DIMER
nummols 96
beads 2
solp 0.0 0.0 0.0
solm 0.1 0.0 0.0
bonds 1
harm 1 2 5.0 0.0
finish
INTERACTIONS 3
solp solp dpd 25.0 1.0 4.5
solm solm dpd 25.0 1.0 4.5
solp solm dpd 25.0 1.0 4.5
CLOSE
.. _dimers:
##########################
Test case: a dimer solvent
##########################
.. image:: ./dimer_fluid.jpg
:width: 10 %
:align: left
Here we describe a physical system in which the software modules dealing with
charge dipole moments in DPD simulations can be tested.
It is a *polarizable fluid* made of harmonically bonded dimers
:math:`(+q,-q)`, pictorially represented on the left (not in scale).
Fixing appropriately the partial charge :math:`q`
and the Bjerrum length :math:`l_B`, this system mimics *water in an oil
background*, as long as the dielectric properties are concerned.
We recall that the electric permittivity is :math:`\epsilon_0` for vacuum, and
:math:`\epsilon<\epsilon_0` for a medium. The medium effect can be split into
a background and a relative term :math:`\epsilon/\epsilon_0=\epsilon_b\epsilon_r`.
The background is constant and uniform, whereas the explicit term is due to
dynamic microscopic objects (dimers in this case) which carry a charge dipole
moment. The strength of electrostatic interactions in a background is set by the bare Bjerrum length :math:`l_B=e^2/(4
\pi\epsilon_0 \epsilon_b k_BT)`. On the other hand, from linear response theory, the bulk value of the relative permittivity is
:math:`\epsilon_r = 1 + \frac{\langle\vec{P}^2\rangle_{\vec{E}=\vec{0}}}{3\epsilon_0\epsilon_{b}\, k_BT\,V}`,
where tin-foil boundary conditions are assumed.
Two types of beads are present in the simulation, `solp` and `solm`, the solvent positive
and negative partial charges, respectively. We fix the bare Bjerrum length
:math:`l_B=42` (appropriate for oil [1]_), the repulsion parameter :math:`A=25`, the harmonic spring
constant :math:`k=5`, the bead density :math:`\rho=3`, the partial charges :math:`|q|=0.46` and the Gaussian
smearing length :math:`\sigma=0.5`. All quantities are given in DPD units,
where :math:`k_BT=1`, :math:`r_c=1` and :math:`m=1`.
This fluid has a relative permittivity :math:`\epsilon_r\simeq 40`, as can be checked
using the ``gen_dipole.f90`` utility. This value is compatible with the ratio
of water and oil permittivities :math:`\epsilon^{water}/\epsilon^{oil}\simeq 40`.
The FIELD file defining the composition and interactions for a system of
volume :math:`V=64` is
.. literalinclude:: ./FIELD
.. [1] Notice that the physical length scale is set choosing :math:`r_c`: if we choose :math:`r_c=0.646nm`
(appropriate to match water density at room temperature if :math:`N_m=3`, i.e., one bead represents
three water molecules), the Bjerrum length of oil in DPD units is :math:`l_B=27 nm\simeq 42 r_c`,
hence the value given above for the oil background.
This diff is collapsed.
Number of nodes used in calculations ?
nchist: 0 96 0 0 0 0 0 0 0 0
Charges for SPECIES type solp :
Charges for SPECIES type solm :
chg= 0.4600 -0.4600
Number of time steps in autocorrelation profile?
switch for FFT computation? (1=yes, 0 or any other integer=no)
.. _dipole_af:
#######################################################################
Autocorrelation functions of charge dipole moments in DL_MESO_DPD
#######################################################################
.. sidebar:: Software Technical Information
Language
FORTRAN 90
Licence
BSD
Documentation Tool
RST and LaTex-generated .pdf file
Application Documentation
:download:`Click to download the manual <manaf.pdf>` with more details
Relevant Training Material
See the Testing section
.. contents:: :local:
Purpose of Module
_________________
This module, ``gen_dipoleaf.f90``, is a generalization of the ``dipoleaf.f90`` post-processing
utility of DL_MESO_DPD, the Dissipative Particle Dynamics (DPD) code from the DL_MESO_ package.
It processes the trajectory (HISTORY) files to obtain the charge dipole moments
of all the (neutral) molecules in the system, and subsequently computes
the dipole autocorrelation functions (DAFs) for each molecule type.
It produces a file `DIPAFDAT` containing both the un-normalized and normalized
DAFs, and, optionally, a file `DIPAFFFT` containing the
Fourier transform (FT) of the latter.
The module can be applied to systems including molecules with a generic charge structure, as long
as each molecule is neutral (otherwise the charge dipole moment would be
frame-dependent) [1]_. **CAVEAT**: this module only analyzes molecular trajectories. If a charged molecule
is present, an error message will be given, while unbonded charges would not be
detected and would lead to erroneous results. Therefore please keep in mind
**to not apply** the module to systems with unbonded charges.
The charge dipole moment of a neutral molecule is :math:`\vec{p}_{mol}=\sum_{i\in mol}q_i \vec{r}_i` where
:math:`\vec{r}_i` are the bead positions and :math:`q_i` their charges. The
total charge dipole moment of the simulated volume :math:`V` is
:math:`\vec{P}=\sum_{mol\in V} \vec{p}_{mol}`.
If more than one molecular species are present, one can split :math:`\vec{P}`
into the different species contributions: :math:`\vec{P}=\sum_{j = 1}^{nmoldef} \vec{P}_j`.
Given a scalar quantity `A`, its non-normalized autocorrelation function (AF)
is :math:`C_{AA}(t) = \langle A(0)A(t)\rangle`, where :math:`\langle\dots\rangle`
indicates an average over trajectories. The normalized one is
:math:`c_{AA}(t) = \frac {\langle A(0)A(t)\rangle}{\langle A(0)A(0)\rangle} = \frac{C_{AA}(t)}{C_{AA}(0)}` [2]_.
Here for the :math:`j` -th molecular species we replace :math:`A` with
:math:`\vec{P}_j`, and the product with a scalar product.
In this case the average over trajectories translates into a sum over different time origins.
The output file `DIPAFDAT` contains the DAFs for each molecular species and,
at the end of the file, the DAF for the system *total* charge dipole moment :math:`\vec{P}`.
The output file `DIPAFFFT` contains the FT of these functions, in the same order.
More in detail, the header of the file `DIPAFDAT` contains the simulation title and a line with the
number of snapshots in HISTORY and of those used for the AFs (`naf`). Then a block follows for each
molecule type, started by the *{molecule name}*, then three columns of data,
:math:`t, C_{\vec{P}\vec{P}},c_{\vec{P}\vec{P}}`.
It is intended that in any block only the contribution to :math:`\vec{P}` from