Merge pull request i-pi#376 from V-Alizade/xtb

add xtb driver to python drivers

drivers/py/pes/xtb.py

@@ -0,0 +1,83 @@
+"""
+Interface with tblite to provide GFN1-xTB and GFN2-xTB calculators.
+
+Example:: 
+
+    python driver.py -m xtb -u -o '{"method": "GFN2-xTB", "numbers": [8,1,1], "periodic": false}'
+"""
+
+import numpy as np
+import json
+
+from ipi.utils.units import unit_to_internal, unit_to_user
+
+try:
+    import tblite.interface as tb
+except ImportError as e:
+    raise ModuleNotFoundError(
+        "Could not find tblite for xtb driver. Please install tblite-python with mamba"
+    ) from e
+
+__DRIVER_NAME__ = "xtb"
+__DRIVER_CLASS__ = "TBLiteDriver"
+
+
+class TBLiteDriver(object):
+    """Base class providing the structure of a PES for the python driver."""
+
+    def __init__(
+        self,
+        args="",
+        verbose=False,
+    ):
+        """Initialized dummy drivers"""
+        config = json.loads(args)
+        try:
+            self.method = config["method"]
+            self.numbers = np.asarray(config["numbers"])
+        except KeyError as e:
+            raise ValueError(f"Required key {str(e)} not found.")
+        self.charge = config.get("charge")
+        self.uhf = config.get("uhf")
+        self.periodic = config.get("periodic")
+        self.verbosity = 1 if verbose else 0
+
+    def __call__(self, cell, pos):
+        """
+        Get energies, forces, and stresses from the tblite library
+        This routine assumes that the client will take positions
+        in bohr, and return energies in hartree, and forces
+        in hartree/abohr.
+        """
+
+        pos = unit_to_user("length", "atomic_unit", pos)
+        cell = unit_to_user("length", "atomic_unit", cell.T)
+
+        calc = tb.Calculator(
+            self.method,
+            self.numbers,
+            np.asarray(pos),
+            self.charge,
+            self.uhf,  # unpaired electrons
+            np.asarray(cell) if self.periodic else None,
+            np.repeat(self.periodic, 3) if self.periodic else None,
+        )
+        calc.set("verbosity", self.verbosity)
+
+        # Do the actual calculation
+        results = calc.singlepoint()
+        pot = results.get("energy")
+        grad = results.get("gradient")
+        vir = results.get("virial")
+
+        # converts to internal quantities
+        pot_ipi = np.asarray(unit_to_internal("energy", "atomic_unit", pot), np.float64)
+        force_ipi = np.asarray(
+            unit_to_internal("force", "atomic_unit", -grad), np.float64
+        )
+        vir_ipi = np.array(
+            unit_to_internal("energy", "atomic_unit", -vir.T), np.float64
+        )
+        extras = ""
+
+        return pot_ipi, force_ipi, vir_ipi, extras

examples/clients/xtb/README.md

@@ -0,0 +1,19 @@
+xtb - i-PI example
+========================
+
+Run a simulation of the methane molecule with GFN2-xTB.
+
+
+A version of the tblite code that is compatible with this example can be 
+obtained with 
+
+```bash
+mamba install tblite-python -c conda-forge
+```
+
+the example can be run as usual
+
+```bash
+i-pi input.xml &> log.ipi &
+i-pi-py_driver -m xtb -o '{"method": "GFN2-xTB", "numbers": [6,1,1,1,1], "periodic": false}' -u -a xtb &> log.xtb &
+```

examples/clients/xtb/ch4.xyz

@@ -0,0 +1,7 @@
+5
+# CELL(abcABC):  100 100 100    90.00000    90.00000    90.00000  cell{atomic_unit}  Traj: positions{angstrom} Step:           9  Bead:       0 
+       C  5.77568e-01  7.10503e-01  5.95431e-01
+       H  1.00494e-04  1.08773e-01  1.29743e+00
+       H  1.28079e+00  1.06096e-01  2.22598e-02
+       H -6.31180e-02  1.31234e+00 -4.92875e-02
+       H  1.80833e+00  2.15490e+00  1.82860e+00

examples/clients/xtb/input.xml

@@ -0,0 +1,46 @@
+<simulation verbosity= "high">
+<output prefix="methane"> 
+<properties stride="5" filename="out">  [ step, time{picosecond},  conserved{electronvolt}, 
+	temperature{kelvin}, kinetic_md{electronvolt}, potential{electronvolt}, pressure_md{bar}, volume{angstrom3}, 
+	ensemble_temperature{kelvin}, cell_abcABC] </properties>
+	<trajectory filename="xc" stride="50" cell_units="angstrom"> x_centroid{angstrom} </trajectory>
+     	<checkpoint stride="1000"/> 
+   	</output> 
+   	<total_steps> 100</total_steps> 
+  	<prng><seed>12345</seed></prng>
+	<ffsocket mode='unix' name='driver'>
+    		<latency>  1.00000000e-04</latency>
+    		<slots>4</slots>
+    		<port>12345</port>
+    		<timeout>60.000000e+00</timeout>
+   		<address>xtb</address>
+  	</ffsocket> 
+	<system>
+        	<initialize nbeads="1">
+                	<file mode="xyz"> ch4.xyz </file>
+                 	<velocities mode="thermal" units="kelvin"> 250.0 </velocities>
+              	</initialize>
+	     	<forces>
+      			<force forcefield='driver'/>
+   		 </forces>
+		<motion mode="dynamics">
+                	<dynamics mode="nvt">
+                    		<timestep units="femtosecond"> 0.5 </timestep>
+                        	<thermostat mode='gle'>
+                        		<A shape='(5,5)'>
+                        					[	
+				4.498098855452e-3,    6.594810718477e-6,    2.788030342989e-4,   -8.808265165053e-4,    5.605371493938e-3,
+                                -6.726802271646e-6,    2.079069559861e-9,    1.746169548818e-5,   -4.800164465960e-6,    1.025830873432e-5,
+                                -3.586191452340e-4,   -1.746169548818e-5,    3.287481976399e-5,    1.245698716799e-4,   -2.417657162526e-4,
+                                -2.508912543565e-4,    4.800164465960e-6,   -1.245698716799e-4,    6.449207766266e-4,    2.783583234046e-4,
+                                5.273493443008e-3,   -1.025830873432e-5,    2.417657162526e-4,   -2.783583234046e-4,    7.488477456790e-3
+                        					]
+                       		</A>
+                        	</thermostat>
+                 	</dynamics>
+              	</motion>
+	   	<ensemble>
+                	<temperature units="kelvin"> 250.0 </temperature>
+           	</ensemble>
+         </system>
+</simulation>

examples/clients/xtb/run.sh

@@ -0,0 +1,7 @@
+#! /bin/bash
+echo "Running i-PI"
+i-pi input.xml &> log.ipi &
+sleep 1
+echo "Running driver"
+i-pi-py_driver -m xtb -o '{"method": "GFN2-xTB", "numbers": [6,1,1,1,1], "periodic": false}' -u -a xtb &> log.xtb 
+