Merge branch 'master' of github.com:ManuelLerchner/MolSim-WS23-24

ManuelLerchner · Dec 15, 2023 · 4e404f2 · 4e404f2
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diff --git a/README.md b/README.md
@@ -86,9 +86,9 @@ In this section we describe how to build the project. You can use the following
 
   - An example run could look like this: `./MolSim ../../body_collision.cub -d 0.0002 -e 5`
 
-  - Further information about the ossible input file formats can be found in the `/docs` directory.
+  - Further information about the possible input file formats can be found in the `/docs` directory.
 
-    - **Note:** Some input file formats can provide own simulation parameters. In the case that the user provides additional parameters via the command line, both sources of parameters are merged. If a conflict occurs, the command line parameters take precedence, since it was explicitly requested by the user.
+    - **Note:** Input files can, and for some cases have to provide own simulation parameters. In case the user provides additional parameters via the command line, both sources of parameters are merged. If a conflict occurs, the command line parameters take precedence, since it was explicitly requested by the user. To avoid mixups, it is recommended to define all parameters in the input file and only use command line for small, temporary adjustments to avoid changing the input file.
 
 ### Run the tests
 

diff --git a/docs/InputFileFormats.md b/docs/InputFileFormats.md
@@ -7,77 +7,12 @@
 Our program supports multiple file formats as input files, which are interpreted differently. The file format is automatically determined by the file extension.
 The following file extensions are supported:
 
-- `.ps`: Contains Raw Particle Data
-- `.cub`: Contains arguments for the internal cuboid generator
 - `.xml`: Contains data for particle generation and allows to specify all the input parameters for the simulation as well
 
 In the following sections, the file formats are explained in detail.
 
 ## File Formats Explained
 
-### .ps
-
-The `.ps` file format contains raw particle data. It is used to directly specify the initial state of the simulation.
-
-- Starts with an arbitrary amount of comment lines, which start with `#` and are only allowed at the beginning of the file
-- The first non-comment line contains a single integer, the number of particles in the simulation
-- Now follow an amount of lines equal to the number of particles, each containing the following arguments (each seperated by spaces):
-  - The particle's position in 3D space (Three floating point numbers, seperated by spaces)
-  - The particle's initial velocity (Three floating point numbers, seperated by spaces)
-  - The particle's mass (A single floating point number the particle's mass)
-
-Note: Floating point numbers can be written in scientific notation, e.g. `1.0e-3` for `0.001`.
-
-An example file could look like this:
-
-```text
-# This is a comment
-# xyz-coord      velocity        mass
-4
-0.0 0.0 0.0      0.0 0.0 0.0     1.0
-0.0 1.0 0.0     -1.0 0.0 0.0     3.0e-6
-0.0 5.36 0.0    -0.425 0.0 0.0   9.55e-4
-34.75 0.0 0.0    0.0 0.0296 0.0  1.0e-14
-```
-
-### .cub
-
-The `.cub` file format contains arguments for the internal cuboid generator. The program uses these arguments to generate one or multiple cuboids of particles given the specified parameters.
-
-- Consists of one or more definitions of cuboids with the following arguments (each on a seperate line), where the values on each line are seperated by spaces:
-  - The coordinate of the lower left front-side corner: '`double` `double` `double`'
-  - Grid Dimensions: '`int` `int` `int`'
-  - Distance of the particles (mesh width): '`double`'
-  - Mass of a single particle: '`double`'
-  - Initial velocity of the particles: '`double` `double` `double`'
-  - Initial temperature of the particles (for temperature dependent wobbling, excludes temperature created by full cuboid velocity) '`double`'
-  - Type of the cuboid: '`int` used for labeling particles in the cuboid'
-- Outside the cuboid definitions an arbitrary amount of comment lines, which start with `#` and empty lines are allowed, furthermore comments are allowed at the end of a line after the last argument
-
-Note: Floating point numbers can be written in scientific notation, e.g. `1.0e-3` for `0.001`.
-
-An example file could look like this:
-
-```text
-# Definition of Cuboid 1
-0.0 0.0 0.0       # Lower left front-side corner
-10 10 10          # Grid Dimensions
-0.1               # Distance of the particles (mesh width)
-1.0               # Mass of a single particle
-0.4 0.0 0.0       # Initial velocity of the particles
-0.0               # Initial temperature
-0                 # Type of the cuboid
-
-# Definition of Cuboid 2
-10.0 10.0 10.0    # Lower left front-side corner
-10 10 10          # Grid Dimensions
-0.1               # Distance of the particles (mesh width)
-1.0               # Mass of a single particle
-0.0 0.4 0.0       # Initial velocity of the particles
-0.0               # Initial temperature
-1                 # Type of the cuboid
-```
-
 ### .xml
 
 The `.xml` file format can be used to specify all the input parameters for the simulation at once. Therefore, it is preferred over the other file formats.
@@ -92,9 +27,9 @@ Its definition is based on the [simulation_schema.xsd](simulation_schema.xsd) fi
   - `<particle_container>` Which particle container implementation should be used
 
 - Particle Data:
-  - `<cuboid_spawner>`: Input data for a cuboid spawner, which generates particles in a cuboid shape
-  - `<sphere_spawner>`: Input data for a sphere spawner, which generates particles in a spherical shape
-  - `<individual_particle>`: Input data for a single particle, which is placed at the specified position
+  - `<cuboid_spawner>`: Input data for a cuboid spawner, which generates particles in a cuboid shape (2 or 3 dimensional)
+  - `<sphere_spawner>`: Input data for a sphere spawner, which generates particles in a spherical shape (2 or 3 dimensional)
+  - `<single_particle_spawner>`: Input data for a single particle, which is placed at the specified position
 
 An example file could look like this:
 

diff --git a/input/body_collision/body_collision_assignment2.cub b/input/body_collision/body_collision_assignment2.cub
diff --git a/input/body_collision/body_collision_assignment2.xml b/input/body_collision/body_collision_assignment2.xml
@@ -0,0 +1,73 @@
+<?xml version="1.0"?>
+<!-- just a sanity check: body collision rewritten to xml -->
+<configuration xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xsi:noNamespaceSchemaLocation="../simulation_schema.xsd">
+
+    <settings>
+        <fps>24</fps>
+        <video_length>30</video_length>
+        <delta_t>0.0002</delta_t>
+        <end_time>5.0</end_time>
+        <third_dimension>false</third_dimension>
+        <particle_container>
+            <directsum_container />
+        </particle_container>
+        <forces>
+            <LennardJones />
+        </forces>
+        <output_format>vtu</output_format>
+    </settings>
+
+
+    <particle_source>
+        <cuboid_spawner>
+            <lower_left_front_corner>
+                <x>0.0</x>
+                <y>0.0</y>
+                <z>0.0</z>
+            </lower_left_front_corner>
+            <grid_dim>
+                <x>40</x>
+                <y>8</y>
+                <z>1</z>
+            </grid_dim>
+            <grid_spacing>1.1225</grid_spacing>
+            <temperature>0.1</temperature>
+            <mass>1</mass>
+            <velocity>
+                <x>0.0</x>
+                <y>0.0</y>
+                <z>0.0</z>
+            </velocity>
+            <type>0</type>
+            <epsilon>5.0</epsilon>
+            <sigma>1.0</sigma>
+        </cuboid_spawner>
+
+        <cuboid_spawner>
+            <lower_left_front_corner>
+                <x>15.0</x>
+                <y>15.0</y>
+                <z>0.0</z>
+            </lower_left_front_corner>
+            <grid_dim>
+                <x>8</x>
+                <y>8</y>
+                <z>1</z>
+            </grid_dim>
+            <grid_spacing>1.1225</grid_spacing>
+            <temperature>0.1</temperature>
+            <mass>1</mass>
+            <velocity>
+                <x>0.0</x>
+                <y>-10.0</y>
+                <z>0.0</z>
+            </velocity>
+            <type>1</type>
+            <epsilon>5.0</epsilon>
+            <sigma>1.0</sigma>
+        </cuboid_spawner>
+
+    </particle_source>
+
+</configuration>
diff --git a/input/periodic_system/eingabe-figure-8.ps b/input/periodic_system/eingabe-figure-8.ps
diff --git a/input/periodic_system/eingabe-figure-8.xml b/input/periodic_system/eingabe-figure-8.xml
@@ -0,0 +1,78 @@
+<?xml version="1.0"?>
+<!-- just a sanity check: body collision rewritten to xml -->
+<configuration xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xsi:noNamespaceSchemaLocation="../simulation_schema.xsd">
+
+    <settings>
+        <fps>24</fps>
+        <video_length>30</video_length>
+        <delta_t>0.0005</delta_t>
+        <end_time>20.0</end_time>
+        <third_dimension>false</third_dimension>
+        <particle_container>
+            <directsum_container />
+        </particle_container>
+        <forces>
+            <Gravitational />
+        </forces>
+        <output_format>vtu</output_format>
+    </settings>
+
+
+    <particle_source>
+        <single_particle_spawner>
+            <position>
+                <x>-1.0</x>
+                <y>0.0 </y>
+                <z>0.0</z>
+            </position>
+            <temperature>0</temperature>
+            <mass>1</mass>
+            <velocity>
+                <x>0.347113</x>
+                <y>0.532727</y>
+                <z>0.0</z>
+            </velocity>
+            <type>0</type>
+            <epsilon>1.0</epsilon>
+            <sigma>1.2</sigma>
+        </single_particle_spawner>
+
+        <single_particle_spawner>
+            <position>
+                <x>1.0</x>
+                <y>0.0 </y>
+                <z>0.0</z>
+            </position>
+            <temperature>0</temperature>
+            <mass>1</mass>
+            <velocity>
+                <x>0.347113</x>
+                <y>0.532727</y>
+                <z>0.0</z>
+            </velocity>
+            <type>1</type>
+            <epsilon>1.0</epsilon>
+            <sigma>1.2</sigma>
+        </single_particle_spawner>
+
+        <single_particle_spawner>
+            <position>
+                <x>0.0</x>
+                <y>0.0 </y>
+                <z>0.0</z>
+            </position>
+            <temperature>0</temperature>
+            <mass>1</mass>
+            <velocity>
+                <x>-0.694226</x>
+                <y>-1.065454</y>
+                <z>0.0</z>
+            </velocity>
+            <type>2</type>
+            <epsilon>1.0</epsilon>
+            <sigma>1.2</sigma>
+        </single_particle_spawner>
+    </particle_source>
+
+</configuration>
diff --git a/src/io/input/FileInputHandler.cpp b/src/io/input/FileInputHandler.cpp
@@ -21,11 +21,7 @@ std::tuple<std::vector<Particle>, std::optional<SimulationParams>> FileInputHand
 
     std::unique_ptr<FileReader> file_reader;
 
-    if (file_extension == ".ps") {
-        file_reader = std::make_unique<PsFileReader>();
-    } else if (file_extension == ".cub") {
-        file_reader = std::make_unique<CubFileReader>();
-    } else if (file_extension == ".xml") {
+    if (file_extension == ".xml") {
         file_reader = std::make_unique<XMLFileReader>(fresh, allow_recursion);
     } else if (file_extension == ".chkpt") {
         file_reader = std::make_unique<ChkptPointFileReader>();

diff --git a/src/io/input/FileInputHandler.h b/src/io/input/FileInputHandler.h
@@ -5,8 +5,6 @@
 
 #include "io/input/InputFormats.h"
 #include "io/input/chkpt/ChkptPointFileReader.h"
-#include "io/input/custom_formats/cub/CubFileReader.h"
-#include "io/input/custom_formats/ps/PsFileReader.h"
 #include "io/input/xml/XMLFileReader.h"
 #include "simulation/SimulationParams.h"
 

diff --git a/src/io/input/InputFormats.cpp b/src/io/input/InputFormats.cpp
@@ -1,3 +1,3 @@
 #include "InputFormats.h"
 
-const std::set<std::string> get_supported_input_file_extensions() { return {".ps", ".cub", ".xml", ".chkpt"}; }
+const std::set<std::string> get_supported_input_file_extensions() { return {".xml", ".chkpt"}; }
diff --git a/src/io/input/custom_formats/FileLineReader.cpp b/src/io/input/custom_formats/FileLineReader.cpp