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Created September 14, 2023 02:57
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Avogadro Batch Render Orbitals
import json
import socket
import struct
import glob
import tempfile
import os
import time
class Connection:
'''Process a JSON-RPC request'''
def __init__(self, name="avogadro"):
Connect to the local named pipe
:param name: The name of the named pipe.
# create socket
self.sock = socket.socket(socket.AF_UNIX, socket.SOCK_STREAM)
# connect
self.sock.connect(tempfile.gettempdir() + "/" + name)
def send_json(self, obj):
Send a JSON-RPC request to the named pipe.
:param obj: The JSON-RPC request object.
def send_message(self, msg):
Send a message to the named pipe
:param msg: The message to send.
size = len(msg)
header = struct.pack(">I", size)
packet = header + msg.encode("ascii")
def receive_message(self, size=1024):
Receive a message from the named pipe.
:param size: The maximum size of the message to receive.
packet = self.sock.recv(size)
return packet[4:]
def recv_json(self):
'''Receive a JSON-RPC response'''
msg = self.recv_message()
return json.loads(msg)
except Exception as exception:
print("error: " + str(exception))
return {}
def close(self):
'''Close the socket to the named pipe'''
def sendMessage(method, options):
conn = Connection()
conn.send_json({"jsonrpc": "2.0", "id": 0, "method": method, "params": options})
reply = str(conn.receive_message())
return reply
if __name__ == "__main__":
conn = Connection()
# render the orbital
options = {
"orbital": "homo",
"isovalue": 0.003
cwd = os.getcwd()
for fileName in glob.glob("*.fchk"):
# open the file
print("Opening " + fileName)
path = cwd + "/" + fileName
basename = path[:-5] # strip off the .fchk
sendMessage("openFile", {"fileName": path})
sendMessage("renderOrbital", options)
# wait 1 minute to compute the surface
# .. adjust as needed
print("Saving HOMO")
sendMessage("saveGraphic", { "fileName": basename + "-homo.png" })
# also render the electron density
sendMessage("renderElectronDensity", {"isovalue": 0.003})
# wait 1 minute to compute the surface
print("Saving Electron Denisty")
sendMessage("saveGraphic", { "fileName": basename + "-edens.png" })
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