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Added option for writing to XTC file #36

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merged 1 commit into from
Dec 7, 2023
Merged

Added option for writing to XTC file #36

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23 changes: 15 additions & 8 deletions openmmsetup/openmmsetup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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')
Expand Down Expand Up @@ -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'
Expand Down Expand Up @@ -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']))
Expand Down Expand Up @@ -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:
Expand Down
35 changes: 27 additions & 8 deletions openmmsetup/templates/simulationOptions.html
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Original file line number Diff line number Diff line change
Expand Up @@ -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">
Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -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;
Expand Down