Centering rises

Author: Jerboa-app

DOCUMENTATION.md

@@ -32,7 +32,7 @@ sfoav struct.xyz
 > [!important]
 > SFOAV can process ```.xyz```, ```.extxyz```, and DL_POLY ```CONFIG```, ```REVCON``` and ```HISTORY``` files. If the file name does not match these patterns all types will be attempted.
 
-This will bring up the view centring the atoms in ```struct.xyz``` in the first frame (if applicable). The camera is centered on (0, 0, 0) and can be moved in spherical coordinates relative to it. The atoms can also be translated relative to (0, 0, 0).
+This will bring up the view centring the atoms in ```struct.xyz``` in the first frame (if applicable). The camera is centered on (0, 0, 0) and can be moved in spherical coordinates relative to it. By defaul the atoms are centred at (0, 0, 0). The atoms can also be translated relative to (0, 0, 0).
 
 > [!note]
 > Reading of structure files is done in a background thread. For large structure files you may be presented with a loading screen. An intel i7-4790K and Kingston A400 SATA SSD is capable of around 1,000,000 (positions only) atoms per second read.

README.md

@@ -31,7 +31,7 @@ sfoav struct.xyz
 > [!important]
 > SFOAV can process ```.xyz```, ```.extxyz```, and DL_POLY ```CONFIG```, ```REVCON``` and ```HISTORY``` files. If the file name does not match these patterns all types will be attempted.
 
-This will bring up the view centring the atoms in ```struct.xyz``` in the first frame (if applicable). The camera is centered on (0, 0, 0) and can be moved in spherical coordinates relative to it. The atoms can also be translated relative to (0, 0, 0).
+This will bring up the view centring the atoms in ```struct.xyz``` in the first frame (if applicable). The camera is centered on (0, 0, 0) and can be moved in spherical coordinates relative to it. By defaul the atoms are centred at (0, 0, 0). The atoms can also be translated relative to (0, 0, 0).
 
 > [!note]
 > Reading of structure files is done in a background thread. For large structure files you may be presented with a loading screen. An intel i7-4790K and Kingston A400 SATA SSD is capable of around 1,000,000 (positions only) atoms per second read.

include/commandLine.h

@@ -448,6 +448,7 @@ struct CommandLine
     Argument<bool> play = {"play", "Set to play trajectories at start up (toggle-able at runtime).", false, false};
     Argument<uint64_t> bondFocus = {"bondFocus", "Only draw bonds involving this atom index.", NULL_INDEX, false};
     Argument<uint8_t> speed = {"speed", "Play speed between 1 and 60.", 60, false};
+    Argument<bool> noCentering = {"noCentering", "Do not centre the atoms", false, false};
 
     /**
      * @brief Determine if help or licenses should be printed.
@@ -532,6 +533,8 @@ struct CommandLine
           << argumentHelp(resolution)
           << "\n"
           << argumentHelp(speed)
+          << "\n"
+          << argumentHelp(noCentering)
           << "\n";
         std::cout << h.str();
     }

src/main.cpp

@@ -53,6 +53,7 @@ int main(int argv, char ** argc)
 
     std::unique_ptr<Structure> structure;
     readStructureFile(options.structure.value, structure);
+    glm::vec3 com = glm::vec3(0);
 
     if (!options.colourmap.value.empty())
     {
@@ -103,6 +104,7 @@ int main(int argv, char ** argc)
         std::cout << "Element " << e << " emphasis bound to key " << keyCodes.at(GLFW_KEY_1+i) << "\n";
     }
     applyColours(structure->atoms, atomColourOverrides);
+    if (!options.noCentering.value) { center(structure->atoms); }
 
     std::vector<Bond> bonds;
     std::vector<uint64_t> bondsFor;
@@ -193,6 +195,7 @@ int main(int argv, char ** argc)
             playBackward = false;
             if (!readInProgress)
             {
+                com = getCenter(structure->atoms);
                 structure->readFrame(structure->framePosition());
                 readInProgress = true;
             }
@@ -203,6 +206,7 @@ int main(int argv, char ** argc)
             playBackward = true;
             if (!readInProgress)
             {
+                com = getCenter(structure->atoms);
                 backward(structure);
                 readInProgress = true;
             }
@@ -249,6 +253,8 @@ int main(int argv, char ** argc)
         {
             // Previous threaded read is done.
             readInProgress = false;
+            if (!options.noCentering.value) { center(structure->atoms); }
+            translate(structure->atoms, com);
             if (options.bondCutoff.value > 0.0)
             {
                 bonds = determineBonds(bondsFor, structure->atoms, options.bondCutoff.value);
@@ -322,6 +328,7 @@ int main(int argv, char ** argc)
 
             if (t >= uint8_t(60)-std::min(options.speed.value, uint8_t(60)))
             {
+                com = getCenter(structure->atoms);
                 if (playBackward)
                 {
                     backward(structure);