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# Code Configuration
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Code Configuration
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*************************
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Basic operation mode
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============================
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... | ... | @@ -46,7 +46,7 @@ periodic boundary conditions |
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These options can be used to distort the simulation cube along the
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given direction with the given factor into a parallelepiped of arbitrary aspect
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ratio. The box size in the given direction increases from the value in the
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parameterfile by the factor given (e.g. if Boxsize is set to 100 and ``LONG_X=4``
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parameter file by the factor given (e.g. if ``Boxsize`` is set to 100 and ``LONG_X=4``
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is set the simulation domain extends from 0 to 400 along X and from 0 to 100
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along Y and Z.)
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... | ... | @@ -187,7 +187,7 @@ decomposition is disabled. |
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Enables domain decomposition together with ``VORONOI_STATIC_MESH`` (which is
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otherwise then disabled), in case non-gas particle types exist and the use of
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domain decompotions is desired. Note that on one hand it may be advantageous
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domain decompositions is desired. Note that on one hand it may be advantageous
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in case the non-gas particles mix well or cluster strongly, but on the other
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hand the mesh construction that follows the domain decomposition is slow for a
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static mesh, so whether or not using this new flag is overall advantageous
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... | ... | @@ -218,7 +218,7 @@ Refinement |
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===========================
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By default, there is no refinement and derefinement and unless set otherwise,
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the cirterion for refinement/derefenment is a target mass.
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the criterion for refinement/derefinement is a target mass.
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**REFINEMENT_SPLIT_CELLS**
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... | ... | @@ -276,7 +276,7 @@ remaining mesh structures are freed after this step as usual. |
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-----
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Non-standard phyiscs
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Non-standard physics
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====================
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**COOLING**
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... | ... | @@ -293,14 +293,14 @@ This imposes an adaptive floor for the temperature. |
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**USE_SFR**
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Star formation model, turning dense gas into collisionless partices. See
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Star formation model, turning dense gas into collisionless particles. See
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Springel&Hernquist, (2003, MNRAS, 339, 289)
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-----
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**SFR_KEEP_CELLS**
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Do not distroy cell out of which a star has formed.
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Do not destroy cell out of which a star has formed.
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-----
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... | ... | @@ -311,7 +311,7 @@ If nothing is active, no gravity included. |
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**SELFGRAVITY**
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Gravitational intraction between simulation particles/cells.
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Gravitational interaction between simulation particles/cells.
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-----
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... | ... | @@ -342,7 +342,7 @@ Gravity is not treated periodically. |
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**ALLOW_DIRECT_SUMMATION**
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Performes direct summation instead of tree-based gravity if number of active
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Performs direct summation instead of tree-based gravity if number of active
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particles < ``DIRECT_SUMMATION_THRESHOLD`` (= 3000 unless specified differently)
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-----
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... | ... | @@ -414,7 +414,7 @@ which works well independent of the data layout, in particular it can cope |
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well with highly clustered particle distributions that occupy only a small
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subset of the total simulated volume. However, this method is a bit slower
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than the default approach (used when the option is disabled), which is best
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matched for homogenously sampled periodic boxes.
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matched for homogeneously sampled periodic boxes.
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-----
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... | ... | @@ -446,7 +446,7 @@ This is only relevant when ``PLACEHIGHRESREGION`` is activated. The size of |
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the high resolution box will be automatically determined as the minimum size
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required to contain the selected particle type(s), in a "shrink-wrap" fashion.
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This region is be expanded on the fly, as needed. However, in order to prevent
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a situation where this size needs to be enlarged frquently, such as when the
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a situation where this size needs to be enlarged frequently, such as when the
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particle set is (slowly) expanding, the minimum size is multiplied by the
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factor ``ENLARGEREGION`` (if defined). Then even if the set is expanding, this
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will only rarely trigger a recalculation of the high resolution mesh geometry,
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... | ... | @@ -506,7 +506,7 @@ If the tree walk wants to use a 'softened node' (i.e. where the maximum |
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gravitational softening of some particles in the node is larger than the node
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distance and larger than the target particle's softening), the node is opened
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by default (because there could be mass components with a still smaller
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softening hidden in the node). This can cause a subtantial performance penalty
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softening hidden in the node). This can cause a substantial performance penalty
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in some cases. By setting this option, this can be avoided. The code will then
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be allowed to use softened nodes, but it does that by evaluating the
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node-particle interaction for each mass component with different softening
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... | ... | @@ -532,7 +532,7 @@ desired softening length by scaling the type-1 softening with the cube root of |
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the mass ratio. Then, the softening type that is closest to this desired
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softening is assigned to the particle (*choosing only from those softening
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values explicitly input as a SofteningComovingTypeX parameter*). This option
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is primarily useful for zoon simulations, where one may for example lump all
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is primarily useful for zoom simulations, where one may for example lump all
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boundary dark matter particles together into type 2 or 3, but yet provide a
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set of softening types over which they are automatically distributed according
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to their mass. If both ``ADAPTIVE_HYDRO_SOFTENING`` and
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... | ... | @@ -547,7 +547,7 @@ assignment exclude softening type 0. Note: particles that accrete matter |
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When this is enabled, the gravitational softening lengths of hydro cells are
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varied according to their radius. To this end, the radius of a cell is
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multiplied by the parameter ``GasSoftFactor``. Then, the closest softening
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from a logarithmicaly spaced table of possible softenings is adopted for the
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from a logarithmically spaced table of possible softenings is adopted for the
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cell. The minimum softening in the table is specified by the parameter
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``MinimumComovingHydroSoftening``, and the larger ones are spaced a factor
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``AdaptiveHydroSofteningSpacing`` apart. The resulting minimum and maximum
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... | ... | @@ -789,7 +789,7 @@ Sum(2^type) for the primary dark matter type. |
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With this option, FOF groups can be augmented by particles/cells of other
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particle types that they "enclose". To this end, for each particle among the
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types selected by the bit mask specifed with ``FOF_SECONDARY_LINK_TYPES``, the
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types selected by the bit mask specified with ``FOF_SECONDARY_LINK_TYPES``, the
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nearest among ``FOF_PRIMARY_LINK_TYPES`` is found and then the particle is
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attached to whatever group this particle is in. sum(2^type) for the types
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linked to nearest primaries.
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... | ... | @@ -802,7 +802,7 @@ An option to make the secondary linking work better in zoom runs (after the |
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FOF groups have been found, the tree is newly constructed for all the
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secondary link targets). This should normally be set to all dark matter
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particle types. If not set, it defaults to ``FOF_PRIMARY_LINK_TYPES``, which
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reproduces the old behaviour.
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reproduces the old behavior.
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-----
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... | ... | @@ -830,7 +830,7 @@ Sort fuzz particles by nearest group and generate offset table in catalog |
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Normally, the snapshots produced with a FOF group catalogue are stored in
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group order, such that the particle set making up a group can be inferred as a
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contiguous block of particles in the snapsot file, making it redundant to
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contiguous block of particles in the snapshot file, making it redundant to
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separately store the IDs of the particles making up a group in the group
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catalogue. By activating this option, one can nevertheless force to create the
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corresponding lists of IDs as part of the group catalogue output.
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... | ... | @@ -851,7 +851,7 @@ within each group. |
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**SAVE_HSML_IN_SNAPSHOT**
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When activated, this will store the hsml-values used for estimating total
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matter density around every point and the corresonding densities in the
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matter density around every point and the corresponding densities in the
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snapshot files associated with a run of Subfind.
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-----
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... | ... | @@ -870,13 +870,13 @@ set together with ``SAVE_HSML_IN_SNAPSHOT``. |
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Additional calculations are carried out, which may be expensive.
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(i) Further quantities related to the angular momentum in different components.
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(ii) The kinetic, thermal and potential binding energies for sperical
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(ii) The kinetic, thermal and potential binding energies for spherical
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overdensity halos.
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-----
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Special behaviour
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Special behavior
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============================
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**RUNNING_SAFETY_FILE**
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... | ... | @@ -938,7 +938,7 @@ This can be used to load SPH ICs that contain identical particle coordinates. |
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**RECOMPUTE_POTENTIAL_IN_SNAPSHOT**
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Needed for postprocess option 18 that can be used to calculate potential
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Needed for post-processing option 18 that can be used to calculate potential
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values for a snapshot.
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-----
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... | ... | @@ -1059,14 +1059,14 @@ Reads in dark matter particles as gas cells. |
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**TILE_ICS**
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Tile ICs by TileICsFactor (specified as paramter) in each dimension.
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Tile ICs by TileICsFactor (specified as parameter) in each dimension.
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-----
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Output fields
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==========================
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Default output filds are: ``position``, ``velocity``, ``ID``, ``mass``,
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Default output fields are: ``position``, ``velocity``, ``ID``, ``mass``,
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``specific internal energy`` (gas only), ``density`` (gas only)
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**OUTPUT_TASK**
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... | ... | @@ -1119,7 +1119,7 @@ Output of velocity of mesh-generating point. |
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**OUTPUT_VOLUME**
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Output of volume of cells; note that this can always be computat as both, density
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Output of volume of cells; note that this can always be computed as both, density
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and mass of cells are by default in output.
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-----
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... | ... | @@ -1171,7 +1171,7 @@ Output of particle softenings. |
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**OUTPUTGRAVINTERACTIONS**
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Output of gravitatational interactions (from the gravitational tree) of particles.
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Output of gravitational interactions (from the gravitational tree) of particles.
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-----
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... | ... | @@ -1208,7 +1208,7 @@ Output of vorticity of gas. |
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**OUTPUT_CSND**
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Output of sound speed. This field is only used for tree-based timesteps!
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Calculate from hydro quantities in postprocessing if required for science
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Calculate from hydro quantities in post-processing if required for science
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applications.
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-----
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... | ... | @@ -1218,7 +1218,7 @@ Output options |
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**PROCESS_TIMES_OF_OUTPUTLIST**
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Goes through times of output list prior to starting the simulaiton to ensure
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Goes through times of output list prior to starting the simulation to ensure
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that outputs are written as close to the desired time as possible (as opposed
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to at next possible time if this flag is not active).
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... | ... | @@ -1227,7 +1227,7 @@ to at next possible time if this flag is not active). |
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**REDUCE_FLUSH**
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If enabled files and stdout are only flushed after a certain time defined in
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the parameter file (standard behaviour: everything is flashed most times
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the parameter file (standard behavior: everything is flushed most times
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something is written to it).
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-----
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... | ... | @@ -1235,7 +1235,7 @@ something is written to it). |
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**OUTPUT_EVERY_STEP**
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Create snapshot on every (global) synchronization point, independent of
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parameters choosen or output list.
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parameters chosen or output list.
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-----
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... | ... | @@ -1286,7 +1286,7 @@ Reports readjustments of buffer sizes. |
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Re-gridding
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============================
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These opitions are auxiliary modes to prepare/convert/relax initial conditions
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These options are auxiliary modes to prepare/convert/relax initial conditions
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and will not carry out a simulation.
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**MESHRELAX**
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