Add MultiGradient node and implement improvements and bug fixes for K…

…DTree and Memory nodes (#53)

* add pre-interaction layers option to hippynn

* revert pre-interaction layers, add fuzzy histogram feature

* fix minor typos, add number pairs to warn_if_under function

* add pair-finder with memory, fix minor bugs

* fix bug in pair-finder with memory

* * New KD Tree pair-finder node
* Modularized pair-finder memory component
* Typos corrected

* revert my change to .gitignore, revise docstring

* Updae change log and docs. Revert unneeded changes.

* add multi gradient node

* add user warning and position wrapping to KDTreePairs+, attribute access to Memory pair-finders

* separate MultiGradient module from Gradient module

* correct PairMemory module to handle batch size > 1, fix bug in inputs sent to KDTree caused by rare rounding issue

* fix auto modlule kwargs in PeriodicPairIndexerMemory class

* Remove KDTree debugging as fix is working

* Update change log

---------

Co-authored-by: Emily Suzanne Shinkle <[email protected]>

CHANGELOG.rst

@@ -7,11 +7,28 @@ New Features:
 - Add nodes for non-adiabatic coupling vectors (NACR) and phase-less loss.
   See /examples/excited_states_azomethane.py.
 
-Improvements
-------------
+- New MultiGradient node for computing multiple partial derivatives of 
+  the same node simultaneously.
+
+Improvements:
+-------------
 
 - Multi-target dipole node now has a shape of (n_molecules, n_targets, 3).
 
+- Add out-of-range warning to FuzzyHistogrammer.
+
+- Create Memory parent class to remove redundancy.
+
+Bug Fixes:
+----------
+
+- Fix KDTreePairs issue caused by floating point precision limitations.
+
+- Fix KDTreePairs issue with not moving tensors off GPU.
+
+- Enable PairMemory nodes to handle batch size > 1.
+
+
 0.0.2a2
 =======
 
@@ -27,8 +44,8 @@ New Features:
 - New KDTreePairs and KDTreePairsMemory nodes for computing pairs using linearly-
   scaling KD Tree algorithm. 
 
-Improvements
-------------
+Improvements:
+-------------
 
 - ASE database loader added to read any ASE file or list of ASE files.
 

hippynn/graphs/nodes/pairs.py

@@ -68,7 +68,23 @@ def __init__(self, name, parents, dist_hard_max, module="auto", module_kwargs=No
         parents = self.expand_parents(parents)
         super().__init__(name, parents, module=module, **kwargs)
 
-class PeriodicPairIndexerMemory(PeriodicPairIndexer):
+class Memory:
+    @property
+    def skin(self):
+        return self.torch_module.skin
+
+    @skin.setter
+    def skin(self, skin):
+        self.torch_module.skin = skin
+
+    @property
+    def reuse_percentage(self):
+        return self.torch_module.reuse_percentage
+
+    def reset_reuse_percentage(self):
+        self.torch_module.reset_reuse_percentage()
+
+class PeriodicPairIndexerMemory(PeriodicPairIndexer, Memory):
     '''
     Implementation of PeriodicPairIndexer with additional memory component.
 
@@ -86,9 +102,9 @@ class PeriodicPairIndexerMemory(PeriodicPairIndexer):
     def __init__(self, name, parents, dist_hard_max, skin, module="auto", module_kwargs=None, **kwargs):
         if module_kwargs is None:
             module_kwargs = {}
-        module_kwargs = {"skin": skin, **module_kwargs}
+        self.module_kwargs = {"skin": skin, **module_kwargs}
 
-        super().__init__(name, parents, dist_hard_max, module=module, module_kwargs=module_kwargs, **kwargs)
+        super().__init__(name, parents, dist_hard_max, module=module, module_kwargs=self.module_kwargs, **kwargs)
 
 
 class ExternalNeighborIndexer(ExpandParents, PairIndexer, AutoKw, MultiNode):
@@ -379,7 +395,7 @@ class KDTreePairs(_DispatchNeighbors):
     '''
     _auto_module_class = pairs_modules.dispatch.KDTreeNeighbors
 
-class KDTreePairsMemory(_DispatchNeighbors):
+class KDTreePairsMemory(_DispatchNeighbors, Memory):
     '''
     Implementation of KDTreePairs with an added memory component.
 

hippynn/graphs/nodes/physics.py

@@ -39,6 +39,31 @@ def __init__(self, name, parents, sign, module="auto", **kwargs):
         self.sign = sign
         self._index_state = position._index_state
         super().__init__(name, parents, module=module, **kwargs)
+
+class MultiGradientNode(AutoKw, MultiNode):
+    """
+    Compute the gradient of a quantity.
+    """
+
+    _auto_module_class = physics_layers.MultiGradient
+
+    def __init__(self, name: str, molecular_energies_parent: _BaseNode, generalized_coordinates_parents: tuple[_BaseNode], signs: tuple[int], module="auto", **kwargs):
+        if isinstance(signs, int):
+            signs = (signs,)
+
+        self.signs = signs
+        self.module_kwargs = {"signs": signs}
+
+        parents = molecular_energies_parent, *generalized_coordinates_parents
+
+        for parent in generalized_coordinates_parents:
+            parent.requires_grad = True        
+
+        self._input_names = tuple((parent.name for parent in parents))
+        self._output_names = tuple((parent.name + "_grad" for parent in generalized_coordinates_parents))
+        self._output_index_states = tuple(parent._index_state for parent in generalized_coordinates_parents)
+
+        super().__init__(name, parents, module=module, **kwargs)
 
 
 class StressForceNode(AutoNoKw, MultiNode):

hippynn/layers/indexers.py

@@ -2,6 +2,7 @@
 Layers for encoding, decoding, index states, besides pairs
 """
 
+import warnings
 import torch
 
 
@@ -249,7 +250,23 @@ def __init__(self, length, vmin, vmax):
         self.bins = torch.nn.Parameter(torch.linspace(vmin, vmax, length), requires_grad=False)
         self.sigma = (vmax - vmin) / length
 
+        self.vmin = vmin
+        self.vmax = vmax
+
     def forward(self, values):
+        # Warn user if provided values lie outside the range of the histogram bins
+        values_out_of_range = (values < self.vmin) + (values > self.vmax)
+
+        if values_out_of_range.sum() > 0:
+            perc_out_of_range = values_out_of_range.float().mean()
+            warnings.warn(
+                "Values out of range for FuzzyHistogrammer\n"
+                f"Number of values out of range: {values_out_of_range.sum()}\n"
+                f"Percentage of values out of range: {perc_out_of_range * 100:.2f}%\n"
+                f"Set range for FuzzyHistogrammer: ({self.vmin:.2f}, {self.vmax:.2f})\n"
+                f"Range of values: ({values.min().item():.2f}, {values.max().item():.2f})"
+            )
+
         if values.shape[-1] != 1:
             values = values[...,None]
         x = values - self.bins

hippynn/layers/pairs/dispatch.py

@@ -6,6 +6,8 @@
 import numpy as np
 from scipy.spatial import KDTree
 import torch
+import os
+from datetime import datetime
 
 from .open import PairMemory
 
@@ -159,10 +161,21 @@ def neighbor_list_kdtree(cutoff, coords, cell):
         new_cell = cell.clone()
         new_coords = coords.clone()
 
-    # Find pair indices
+    new_coords = new_coords % torch.diag(new_cell)
+
+    # The following three lines are included to prevent an extremely rare but not unseen edge 
+    # case where the modulo operation returns a particle coordinate that is exactly equal to 
+    # the corresponding cell length, causing KDTree to throw an error
+    n_particles = new_coords.shape[0]
+    tiled_cell = torch.tile(torch.diag(new_cell), (n_particles,)).reshape(n_particles, -1)
+    new_coords = torch.where(new_coords == tiled_cell, 0, new_coords)
+
+    new_coords = new_coords.detach().cpu().numpy()
+    new_cell = torch.diag(new_cell).detach().cpu().numpy()
+
     tree = KDTree(
-        data=new_coords.detach().cpu().numpy(), 
-        boxsize=torch.diag(new_cell).detach().cpu().numpy()
+        data=new_coords, 
+        boxsize=new_cell,
     )
 
     pairs = tree.query_pairs(r=cutoff, output_type='ndarray')

hippynn/layers/pairs/open.py

@@ -128,7 +128,11 @@ def initialize_buffers(self):
             self.register_buffer(name=name, tensor=None, persistent=False)
 
     def recalculation_needed(self, coordinates, cells):
-        if self.positions is None: # ie. forward function has not been called
+        if coordinates.shape[0] != 1:  # does not support batch size larger than 1
+            return True
+        if self.positions is None:  # ie. forward function has not been called
+            return True
+        if self.skin == 0:
             return True
         if (self.cells != cells).any() or (((self.positions - coordinates)**2).sum(1).max() > (self._skin/2)**2):
             return True

hippynn/layers/physics.py

@@ -17,7 +17,22 @@ def __init__(self, sign):
 
     def forward(self, molecular_energies, positions):
         return self.sign * torch.autograd.grad(molecular_energies.sum(), positions, create_graph=True)[0]
-
+
+class MultiGradient(torch.nn.Module):
+    def __init__(self, signs):
+        super().__init__()
+        if isinstance(signs, int):
+            signs = (signs,)
+        for sign in signs:
+            assert sign in (-1,1), "Sign of gradient must be -1 or +1"
+        self.signs = signs
+
+    def forward(self, molecular_energies: Tensor, *generalized_coordinates: Tensor):
+        if isinstance(generalized_coordinates, Tensor):
+            generalized_coordinates = (generalized_coordinates,)
+        assert len(generalized_coordinates) == len(self.signs), f"Number of items to take derivative w.r.t ({len(generalized_coordinates)}) must match number of provided signs ({len(self.signs)})."
+        grads = torch.autograd.grad(molecular_energies.sum(), generalized_coordinates, create_graph=True)
+        return tuple((sign * grad for sign, grad in zip(self.signs, grads)))
 
 class StressForce(torch.nn.Module):
     def __init__(self, *args, **kwargs):