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/exceptions.h"
  54
  55 namespace gmx
  56 {
  57
  58 void
  59 OutputRequirementOptionDirector::initOptions(IOptionsContainer        *options)
  60 {
  61     options->addOption(EnumOption<ChangeSettingType>("vel")
  62                            .enumValue(cChangeSettingTypeEnum)
  63                            .store(&velocity_)
  64                            .description("Save velocities from frame if possible"));
  65     options->addOption(EnumOption<ChangeSettingType>("force")
  66                            .enumValue(cChangeSettingTypeEnum)
  67                            .store(&force_)
  68                            .description("Save forces from frame if possible"));
  69     options->addOption(EnumOption<ChangeAtomsType>("atoms")
  70                            .enumValue(cChangeAtomsTypeEnum)
  71                            .store(&atoms_)
  72                            .description("Decide on providing new atom information from topology or using current frame atom information"));
  73     options->addOption(IntegerOption("precision")
  74                            .store(&prec_)
  75                            .defaultValue(prec_)
  76                            .storeIsSet(&setNewPrecision_)
  77                            .description("Set output precision to custom value"));
  78     options->addOption(RealOption("starttime")
  79                            .store(&startTimeValue_)
  80                            .defaultValue(startTimeValue_)
  81                            .timeValue()
  82                            .storeIsSet(&setNewStartTime_)
  83                            .description("Change start time for first frame"));
  84     options->addOption(RealOption("timestep")
  85                            .store(&timeStepValue_)
  86                            .defaultValue(timeStepValue_)
  87                            .timeValue()
  88                            .storeIsSet(&setNewTimeStep_)
  89                            .description("Change time between different frames"));
  90     options->addOption(RealOption("box")
  91                            .vector()
  92                            .storeVector(&newBoxVector_)
  93                            .valueCount(3)
  94                            .storeIsSet(&setNewBox_)
  95                            .description("New diagonal box vector for output frame"));
  96 }
  97
  98 OutputRequirements
  99 OutputRequirementOptionDirector::process() const
 100 {
 101     OutputRequirements requirements;
 102     /* If the user has just set the values directly without setting the flags,
 103      * we set the flags to state that user requested changes are there.*/
 104     if (setNewBox_)
 105     {
 106         requirements.box = ChangeFrameInfoType::Always;
 107         clear_mat(requirements.newBox);
 108         for (int i = 0; i < DIM; ++i)
 109         {
 110             requirements.newBox[i][i] = newBoxVector_[i];
 111         }
 112     }
 113     if (setNewPrecision_)
 114     {
 115         requirements.precision = ChangeFrameInfoType::Always;
 116         requirements.prec      = prec_;
 117     }
 118     if ((setNewTimeStep_ || setNewStartTime_))
 119     {
 120         requirements.startTimeValue = startTimeValue_;
 121         requirements.timeStepValue  = timeStepValue_;
 122         if (setNewTimeStep_ && setNewStartTime_)
 123         {
 124             requirements.frameTime = ChangeFrameTimeType::Both;
 125         }
 126         else if (setNewTimeStep_)
 127         {
 128             requirements.frameTime = ChangeFrameTimeType::TimeStep;
 129         }
 130         else
 131         {
 132             requirements.frameTime = ChangeFrameTimeType::StartTime;
 133         }
 134     }
 135     requirements.atoms    = atoms_;
 136     requirements.velocity = velocity_;
 137     requirements.force    = force_;
 138     return requirements;
 139 }
 140
 141 } // namespace gmx