Merge pull request #36 from peastman/xtc

Added option for writing to XTC file
openmm · Dec 7, 2023 · e736086 · e736086
2 parents 8b13c3b + 4d13c22
commit e736086
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Showing 2 changed files with 42 additions and 16 deletions.
diff --git a/openmmsetup/openmmsetup.py b/openmmsetup/openmmsetup.py
@@ -286,7 +286,7 @@ def showSimulationOptions():
 def setSimulationOptions():
     for key in request.form:
         session[key] = request.form[key]
-    session['writeDCD'] = 'writeDCD' in request.form
+    session['writeTrajectory'] = 'writeTrajectory' in request.form
     session['writeData'] = 'writeData' in request.form
     session['writeCheckpoint'] = 'writeCheckpoint' in request.form
     session['dataFields'] = request.form.getlist('dataFields')
@@ -421,9 +421,10 @@ def configureDefaultOptions():
     session['pressure'] = '1.0'
     session['barostatInterval'] = '25'
     session['nonbondedMethod'] = 'CutoffNonPeriodic' if implicitWater else 'PME'
-    session['writeDCD'] = True
-    session['dcdFilename'] = 'trajectory.dcd'
-    session['dcdInterval'] = '10000'
+    session['writeTrajectory'] = True
+    session['trajFormat'] = 'dcd'
+    session['trajFilename'] = 'trajectory.dcd'
+    session['trajInterval'] = '10000'
     session['writeData'] = True
     session['dataFilename'] = 'log.txt'
     session['dataInterval'] = '1000'
@@ -548,8 +549,11 @@ def write(self, string):
     script.append("platform = Platform.getPlatformByName('%s')" % session['platform'])
     if session['platform'] in ('CUDA', 'OpenCL'):
         script.append("platformProperties = {'Precision': '%s'}" % session['precision'])
-    if session['writeDCD']:
-        script.append("dcdReporter = DCDReporter('%s', %s)" % (session['dcdFilename'], session['dcdInterval']))
+    if session['writeTrajectory']:
+        if session['trajFormat'] == 'dcd':
+            script.append("dcdReporter = DCDReporter('%s', %s)" % (session['trajFilename'], session['trajInterval']))
+        else:
+            script.append("xtcReporter = XTCReporter('%s', %s)" % (session['trajFilename'], session['trajInterval']))
     if session['writeData']:
         args = ', '.join('%s=True' % field for field in session['dataFields'])
         script.append("dataReporter = StateDataReporter('%s', %s, totalSteps=steps," % (session['dataFilename'], session['dataInterval']))
@@ -643,8 +647,11 @@ def _xml_script_segment(to_serialize, target_file):
 
     script.append('\n# Simulate\n')
     script.append("print('Simulating...')")
-    if session['writeDCD']:
-        script.append('simulation.reporters.append(dcdReporter)')
+    if session['writeTrajectory']:
+        if session['trajFormat'] == 'dcd':
+            script.append('simulation.reporters.append(dcdReporter)')
+        else:
+            script.append('simulation.reporters.append(xtcReporter)')
     if session['writeData']:
         script.append('simulation.reporters.append(dataReporter)')
         if isInternal:

diff --git a/openmmsetup/templates/simulationOptions.html b/openmmsetup/templates/simulationOptions.html
@@ -136,16 +136,22 @@
             <div id="output" class="tab-pane fade">
             <p/>
             <div class="form-group">
-            <label><input type="checkbox" name="writeDCD" id="writeDCD" oninput="optionChanged()" {{ 'checked' if session['writeDCD'] else '' }}> Save trajectory to a DCD file</label>
+            <label><input type="checkbox" name="writeTrajectory" id="writeTrajectory" oninput="optionChanged()" {{ 'checked' if session['writeTrajectory'] else '' }}> Save trajectory to a file</label>
             </div>
-            <div id="dcdFileOptions">
+            <div id="trajFileOptions">
                 <div class="form-group">
-                <label for="dcdFilename">DCD Filename</label>
-                {{ textfield('dcdFilename', 'The filename for the trajectory file.') }}
+                <label for="trajFormat">Trajectory Format</label>
+                {{ choice('trajFormat', 'Select format in which to save the trajectory.', [
+                    ('dcd', 'DCD', 'This format stores coordinates most precisely.'),
+                    ('xtc', 'XTC', 'This format stores coordinates with reduced precision, leading to smaller files.')], 'trajectoryFormatChanged') }}
                 </div>
                 <div class="form-group">
-                <label for="dcdInterval">DCD Output Interval (steps)</label>
-                {{ textfield('dcdInterval', 'The interval at which to write frames to the trajectory, measured in time steps.') }}
+                <label for="trajFilename">Trajectory Filename</label>
+                {{ textfield('trajFilename', 'The filename for the trajectory file.') }}
+                </div>
+                <div class="form-group">
+                <label for="trajInterval">Trajectory Output Interval (steps)</label>
+                {{ textfield('trajInterval', 'The interval at which to write frames to the trajectory, measured in time steps.') }}
                 </div>
             </div>
             <div class="form-group">
@@ -264,6 +270,19 @@ <h4 class="modal-title">Platform Not Available</h4>
 </form>
 
 <script>
+function trajectoryFormatChanged() {
+    // Used when <select> for trajFormat changes. This changes the
+    // extension of the file depending on the selected format.
+    var fileLabel = document.getElementById("trajFilename");
+    var asSplit = fileLabel.value.split(".");
+    if (asSplit.length > 1) asSplit.pop();
+    if (asSplit[0] == "") asSplit[0] = "trajectory";  // set default if empty
+    asSplit.push(document.getElementById("trajFormat").value);
+    fileLabel.value = asSplit.join(".");
+
+    optionChanged();
+}
+
 function outputFiletypeChanged() {
     // Used when <select> for finalStateFileType changes. This changes the
     // extension of the file depending on the selected output filetype.
@@ -297,8 +316,8 @@ <h4 class="modal-title">Platform Not Available</h4>
     document.getElementById("barostatIntervalRow").hidden = (ensemble != 'npt');
     platform = document.getElementById("platform").value;
     document.getElementById("precisionRow").hidden = (platform != 'CUDA' && platform != 'OpenCL');
-    writeDCD = document.getElementById("writeDCD").checked;
-    document.getElementById("dcdFileOptions").hidden = !writeDCD;
+    writeTrajectory = document.getElementById("writeTrajectory").checked;
+    document.getElementById("trajFileOptions").hidden = !writeTrajectory;
     writeData = document.getElementById("writeData").checked;
     document.getElementById("logFileOptions").hidden = !writeData;
     writeCheckpoint = document.getElementById("writeCheckpoint").checked;