src/gromacs/coordinateio/requirements.cpp

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  35 /*!\internal
  36  * \file
  37  * \brief
  38  * Implements helper function to populate requirements from user input.
  39  *
  40  * \author Paul Bauer <paul.bauer.q@gmail.com>
  41  * \ingroup module_coordinateio
  42  */
  43
  44 #include "gmxpre.h"
  45
  46 #include "requirements.h"
  47
  48 #include <algorithm>
  49
  50 #include "gromacs/options/basicoptions.h"
  51 #include "gromacs/options/filenameoption.h"
  52 #include "gromacs/options/ioptionscontainer.h"
  53 #include "gromacs/utility/enumerationhelpers.h"
  54 #include "gromacs/utility/exceptions.h"
  55
  56 namespace gmx
  57 {
  58
  59 //! Mapping for enums from \ref ChangeSettingType.
  60 static const EnumerationArray<ChangeSettingType, const char*> c_changeSettingTypeNames = {
  61     { "preserved-if-present", "always", "never" }
  62 };
  63 //! Mapping for enums from \ref ChangeAtomsType.
  64 static const EnumerationArray<ChangeAtomsType, const char*> c_changeAtomsTypeNames = {
  65     { "preserved-if-present", "always-from-structure", "never", "always" }
  66 };
  67 /* Currently unused
  68 //! Mapping for enums from \ref ChangeFrameInfoType.
  69 static const EnumerationArray<ChangeFrameInfoType, const char*> c_changeFrameInfoTypeNames = { {
  70 "preserved-if-present", "always" } };
  71 //! Mapping for values from \ref ChangeFrameTimeType.
  72 static const EnumerationArray<ChangeFrameTimeType, const char*> c_changeFrameTimeTypeNames = { {
  73 "preserved-if-present", "starttime", "timestep", "both" } };
  74 */
  75
  76 void OutputRequirementOptionDirector::initOptions(IOptionsContainer* options)
  77 {
  78     options->addOption(EnumOption<ChangeSettingType>("vel")
  79                                .enumValue(c_changeSettingTypeNames)
  80                                .store(&velocity_)
  81                                .description("Save velocities from frame if possible"));
  82     options->addOption(EnumOption<ChangeSettingType>("force")
  83                                .enumValue(c_changeSettingTypeNames)
  84                                .store(&force_)
  85                                .description("Save forces from frame if possible"));
  86     options->addOption(
  87             EnumOption<ChangeAtomsType>("atoms").enumValue(c_changeAtomsTypeNames).store(&atoms_).description("Decide on providing new atom information from topology or using current frame atom information"));
  88     options->addOption(IntegerOption("precision")
  89                                .store(&prec_)
  90                                .defaultValue(prec_)
  91                                .storeIsSet(&setNewPrecision_)
  92                                .description("Set output precision to custom value"));
  93     options->addOption(RealOption("starttime")
  94                                .store(&startTimeValue_)
  95                                .defaultValue(startTimeValue_)
  96                                .timeValue()
  97                                .storeIsSet(&setNewStartTime_)
  98                                .description("Change start time for first frame"));
  99     options->addOption(RealOption("timestep")
 100                                .store(&timeStepValue_)
 101                                .defaultValue(timeStepValue_)
 102                                .timeValue()
 103                                .storeIsSet(&setNewTimeStep_)
 104                                .description("Change time between different frames"));
 105     options->addOption(RealOption("box")
 106                                .vector()
 107                                .storeVector(&newBoxVector_)
 108                                .valueCount(3)
 109                                .storeIsSet(&setNewBox_)
 110                                .description("New diagonal box vector for output frame"));
 111 }
 112
 113 OutputRequirements OutputRequirementOptionDirector::process() const
 114 {
 115     OutputRequirements requirements;
 116     /* If the user has just set the values directly without setting the flags,
 117      * we set the flags to state that user requested changes are there.*/
 118     if (setNewBox_)
 119     {
 120         requirements.box = ChangeFrameInfoType::Always;
 121         clear_mat(requirements.newBox);
 122         for (int i = 0; i < DIM; ++i)
 123         {
 124             requirements.newBox[i][i] = newBoxVector_[i];
 125         }
 126     }
 127     if (setNewPrecision_)
 128     {
 129         requirements.precision = ChangeFrameInfoType::Always;
 130         requirements.prec      = prec_;
 131     }
 132     if ((setNewTimeStep_ || setNewStartTime_))
 133     {
 134         requirements.startTimeValue = startTimeValue_;
 135         requirements.timeStepValue  = timeStepValue_;
 136         if (setNewTimeStep_ && setNewStartTime_)
 137         {
 138             requirements.frameTime = ChangeFrameTimeType::Both;
 139         }
 140         else if (setNewTimeStep_)
 141         {
 142             requirements.frameTime = ChangeFrameTimeType::TimeStep;
 143         }
 144         else
 145         {
 146             requirements.frameTime = ChangeFrameTimeType::StartTime;
 147         }
 148     }
 149     requirements.atoms    = atoms_;
 150     requirements.velocity = velocity_;
 151     requirements.force    = force_;
 152     return requirements;
 153 }
 154
 155 } // namespace gmx