From dd803bc28ab947e80e922211349c3b4a05b3938c Mon Sep 17 00:00:00 2001
From: dz24 <rubidxx.dz@gmail.com>
Date: Tue, 30 Sep 2025 16:30:47 +0900
Subject: [PATCH] firstdraft

---
 inftools/analysis/Free_energy.py | 24 +++++++++++++++++++++---
 inftools/analysis/Wham_Pcross.py |  3 ++-
 2 files changed, 23 insertions(+), 4 deletions(-)

diff --git a/inftools/analysis/Free_energy.py b/inftools/analysis/Free_energy.py
index bce7a50..ecc5941 100644
--- a/inftools/analysis/Free_energy.py
+++ b/inftools/analysis/Free_energy.py
@@ -28,23 +28,26 @@ def update_histogram(data, factor, histogram, Minx, Miny, dx, dy):
     return histogram
 
 
-def calculate_free_energy(trajlabels, WFtot, Trajdir, outfolder, histo_stuff):
+
+def calculate_free_energy(trajlabels, WFtot, Trajdir, outfolder, histo_stuff, interfaces):
     print("We are now going to perform the Landau Free Energy calculations")
     Nbinsx, Nbinsy = histo_stuff["nbx"], histo_stuff["nby"]
     Maxx, Minx = histo_stuff["maxx"], histo_stuff["minx"]
     Maxy, Miny = histo_stuff["maxy"], histo_stuff["miny"]
     xcol, ycol = histo_stuff["xcol"], histo_stuff["ycol"]
-    
+
     if any(var is None for var in [Nbinsy, Maxy, Miny, ycol]):
         none_vars = [name for name, var in zip(["nby", "maxy", "miny", "ycol"], [Nbinsy, Maxy, Miny, ycol]) if var is None]
         assert all(var is None for var in [Nbinsy, Maxy, Miny, ycol]), \
             f"The following variables are None and should be set: {', '.join(none_vars)}"
     if Nbinsy is not None:
         histogram = np.zeros((Nbinsx, Nbinsy))
+        histogram_comm = np.zeros((Nbinsx, Nbinsy))
         dy = (Maxy - Miny) / Nbinsy
         yval = [Miny + 0.5 * dy + i * dy for i in range(Nbinsy)]
     else:
         histogram = np.zeros(Nbinsx)
+        histogram_comm = np.zeros(Nbinsx)
         dy = None
         yval = None
     dx = (Maxx - Minx) / Nbinsx
@@ -53,8 +56,22 @@ def calculate_free_energy(trajlabels, WFtot, Trajdir, outfolder, histo_stuff):
     for label, factor in zip(trajlabels, WFtot):
         trajfile = Trajdir + "/" + str(label) + "/order.txt"
         data = extract(trajfile, xcol, ycol)
+        data0 = np.loadtxt(trajfile)
         histogram = update_histogram(data, factor, histogram, Minx, Miny, dx, dy)
 
+        # calculate committor, here each path is determined to be reactive
+        # or not based on the initial interfaces and order.txt files
+        # 2 for reactive, 1 for unreactive for now.
+        reactive = 2 if data0[-1, 1] > interfaces[-1] else 1
+        histogram_comm = update_histogram(data, factor*reactive, histogram_comm, Minx, Miny, dx, dy)
+
+    # calculate the committor projection
+    histogram_comm[histogram_comm != 0] /= histogram[histogram_comm != 0]
+
+    # set non-assigned values (0) to np.inf and shift actual values between [0, 1]
+    histogram_comm[histogram_comm == 0] = np.inf
+    histogram_comm -= 1
+
     # normalize such that the highest value equals 1
     max_value = np.max(histogram)
     histogram /= max_value
@@ -63,6 +80,7 @@ def calculate_free_energy(trajlabels, WFtot, Trajdir, outfolder, histo_stuff):
     if not yval is None:
         np.savetxt(os.path.join(outfolder, "histo_yval.txt"), yval)
     np.savetxt(os.path.join(outfolder, "histo_probability.txt"), histogram)
-    
+    np.savetxt(os.path.join(outfolder, "histo_committor.txt"), histogram_comm)
+
     histogram = -np.log(histogram)  # get Landau free energy in kBT units
     np.savetxt(os.path.join(outfolder, "histo_free_energy.txt"), histogram)
diff --git a/inftools/analysis/Wham_Pcross.py b/inftools/analysis/Wham_Pcross.py
index f3914a4..6ba5937 100644
--- a/inftools/analysis/Wham_Pcross.py
+++ b/inftools/analysis/Wham_Pcross.py
@@ -850,6 +850,7 @@ def write_ploc(ofile, rescale, folder=folder):
         WFtot = [a + b for a, b in zip(WHAMfactorsMIN, WHAMfactors)]
         trajlabels = [int(x[0]) for x in matrix]
 
-        calculate_free_energy(trajlabels, WFtot, inp_dic["trajdir"], folder, histo_stuff)
+        calculate_free_energy(trajlabels, WFtot, inp_dic["trajdir"],
+                              folder, histo_stuff, lambda_interfaces)
 
     # Finished!