From f1a7973ad27eb18a3be63a6ade3dfaba53821444 Mon Sep 17 00:00:00 2001
From: Jiao Lin <jiao.lin@gmail.com>
Date: Mon, 29 May 2023 20:38:37 -0700
Subject: [PATCH] added dgs_iqe_monitor.py (it is being used in detector cross
 talk study)

---
 acc/components/monitors/dgs_iqe_monitor.py | 214 +++++++++++++++++++++
 1 file changed, 214 insertions(+)
 create mode 100644 acc/components/monitors/dgs_iqe_monitor.py

diff --git a/acc/components/monitors/dgs_iqe_monitor.py b/acc/components/monitors/dgs_iqe_monitor.py
new file mode 100644
index 0000000..1a2a157
--- /dev/null
+++ b/acc/components/monitors/dgs_iqe_monitor.py
@@ -0,0 +1,214 @@
+# -*- python -*-
+#
+
+category = 'monitors'
+
+import math
+from numba import cuda, void, int64
+import numba as nb, numpy as np
+from mcni.utils.conversion import V2K, SE2V, K2V, VS2E
+from ...config import get_numba_floattype, get_numpy_floattype
+from ...neutron import absorb, prop_z0, e2v
+NB_FLOAT = get_numba_floattype()
+from ...geometry.arrow_intersect import intersectCylinderSide
+
+from .MonitorBase import MonitorBase as base
+class IQE_monitor(base):
+
+    """I(Q,E) monitor for neutron DGS"""
+
+    def __init__(
+            self, name,
+            Ei = 60., L0 = 10,
+            Qmin=0., Qmax=10., nQ=100,
+            Emin=-45., Emax=45., nE=90,
+            max_angle_in_plane = 120, min_angle_in_plane = 0,
+            max_angle_out_of_plane = 30, min_angle_out_of_plane = -30,
+            radius = 3.,
+            filename = "iqe.h5",
+    ):
+        """
+        Initialize this IQE_monitor component.
+        """
+        # assert np.abs(max_angle_out_of_plane) < 60.
+        # assert np.abs(min_angle_out_of_plane) < 60.
+        assert radius > 0.
+        assert L0 > 0.
+        self.name = name
+        self.filename = filename
+        self.Ei = Ei
+        self.L0 = L0
+        self.nQ, self.Qmin, self.Qmax = nQ, Qmin, Qmax
+        self.nE, self.Emin, self.Emax = nE, Emin, Emax
+        dQ = (Qmax-Qmin)/nQ
+        self.Q_centers = np.arange(Qmin+dQ/2, Qmax, dQ)
+        dE = (Emax-Emin)/nE
+        self.E_centers = np.arange(Emin+dE/2, Emax, dE)
+        shape = 3, nQ, nE
+        self.out = np.zeros(shape)
+        self.out_N = self.out[0]
+        self.out_p = self.out[1]
+        self.out_p2 = self.out[2]
+        max_angle = max(
+            np.abs(max_angle_out_of_plane), np.abs(min_angle_out_of_plane)
+        )
+        height = 1.1*2*radius*math.tan(math.radians(max_angle))
+        self.propagate_params = (
+            np.array([
+                Ei, L0, Qmin, Qmax, Emin, Emax,
+                max_angle_in_plane, min_angle_in_plane,
+                max_angle_out_of_plane, min_angle_out_of_plane,
+                radius, height,
+            ]),
+            nQ, nE, self.out
+        )
+
+    def copy(self):
+        (Ei, L0, Qmin, Qmax, Emin, Emax,
+         max_angle_in_plane, min_angle_in_plane,
+         max_angle_out_of_plane, min_angle_out_of_plane,
+         radius, height,
+         ), nQ, nE, out = self.propagate_params
+        return self.__class__(
+            self.name,
+            Ei = Ei, L0=L0,
+            Qmin=Qmin, Qmax=Qmax, nQ=nQ,
+            Emin=Emin, Emax=Emax, nE=nE,
+            max_angle_in_plane = max_angle_in_plane,
+            min_angle_in_plane = min_angle_in_plane,
+            max_angle_out_of_plane = max_angle_out_of_plane,
+            min_angle_out_of_plane = min_angle_out_of_plane,
+            radius = radius,
+            filename=self.filename)
+
+    def getHistogram(self, scale_factor=1.):
+        h = self._getHistogram(scale_factor)
+        n = getNormalization(self, N=None, epsilon=1e-7)
+        import histogram.hdf as hh
+        hh.dump(h, "before-norm.h5")
+        hh.dump(n, "norm.h5")
+        return h/n
+
+    def _getHistogram(self, scale_factor=1.):
+        import histogram as H
+        axes = [('Q', self.Q_centers, '1./angstrom'), ('E', self.E_centers, 'meV')]
+        return H.histogram(
+            'IQE', axes,
+            data=self.out_p*scale_factor,
+            errors=self.out_p2*scale_factor*scale_factor)
+
+    @cuda.jit(
+        void(NB_FLOAT[:], NB_FLOAT[:], int64, int64, NB_FLOAT[:, :, :]),
+        device=True)
+    def propagate(neutron, params, nQ, nE, out):
+        (Ei, L0, Qmin, Qmax, Emin, Emax,
+         max_angle_in_plane, min_angle_in_plane,
+         max_angle_out_of_plane, min_angle_out_of_plane,
+         radius, height) = params
+        x,y,z, vx,vy,vz = neutron[:6]
+        n, t1, t2 = intersectCylinderSide(z,x,y, vz,vx,vy, radius, height)
+        if n == 0: return
+        if n == 2:
+            dt = t2
+        elif n == 1:
+            dt = t1
+        else:
+            return
+        x2 = x + vx*dt
+        y2 = y + vy*dt
+        z2 = z + vz*dt
+        angle_in_plane = math.atan2( x2,z2 )/math.pi*180.
+        if y2!=0:
+            theta = math.atan( math.sqrt(x2*x2+z2*z2)/math.fabs(y2) )/math.pi*180.
+            if y2>0: angle_out_of_plane = 90.-theta
+            else: angle_out_of_plane = theta - 90.
+        else:
+            angle_out_of_plane = 0.
+
+        if min_angle_in_plane < angle_in_plane < max_angle_in_plane \
+	       and min_angle_out_of_plane < angle_out_of_plane < max_angle_out_of_plane:
+            t = neutron[-2] + dt
+            vi = e2v(Ei)
+            t_src2sample = L0/vi
+            t_sample2det = t - t_src2sample
+            dist_sample2det = math.sqrt(x2*x2+y2*y2+z2*z2)
+            # measured velocity
+            m_vf = dist_sample2det/t_sample2det
+            m_vx = x2/dist_sample2det * m_vf
+            m_vy = y2/dist_sample2det * m_vf
+            m_vz = z2/dist_sample2det * m_vf
+            # determine Q and E
+            Q = math.sqrt( m_vx*m_vx + m_vy*m_vy + (m_vz-vi)*(m_vz-vi) )*V2K
+            E = Ei - (m_vf*m_vf) * VS2E
+            # find out the bin numbers and add to the histogram
+            if (Q>=Qmin and Q<Qmax) and (E>=Emin and E<Emax) :
+                iQ=int( math.floor( (Q-Qmin)/(Qmax-Qmin)*nQ ) )
+                iE=int( math.floor( (E-Emin)/(Emax-Emin)*nE ) )
+                p = neutron[-1]
+                cuda.atomic.add(out, (0,iQ,iE), 1)
+                cuda.atomic.add(out, (1,iQ,iE), p)
+                cuda.atomic.add(out, (2,iQ,iE), p*p)
+        return
+
+def getNormalization(monitor, N=None, epsilon=1e-7):
+    # randomly shoot neutrons to monitor in 4pi solid angle
+    print("* start computing normalizer...")
+    if N is None:
+        N = monitor.nQ * monitor.nE * 10000
+    import mcni, random, mcni.utils.conversion as conversion, math, os
+    import numpy as np
+
+    # incident velocity
+    vi = conversion.e2v(monitor.Ei)
+    # monitor copy
+    mcopy = monitor.copy()
+    # send neutrons to monitor copy
+    N1 = 0; dN = int(2e7)
+    print("  - total neutrons needed :", N)
+    while N1 < N:
+        n = min(N-N1, dN)
+        neutrons = makeNeutrons(monitor.Ei, monitor.L0, monitor.Emin, monitor.Emax, n)
+        mcopy.process(neutrons)
+        N1 += n
+        print("  - processed %s" % N1)
+        continue
+    h = mcopy._getHistogram(1.) # /N)
+    # for debug
+    # import histogram.hdf as hh
+    # hh.dump(h, 'tmp.h5', '/', 'c')
+    h.I[h.I<epsilon] = 1
+    #
+    print("  - done computing normalizer")
+    return h
+
+def makeNeutrons(Ei, L0, Emin, Emax, N):
+    import mcni
+    neutrons = mcni.neutron_buffer(N)
+    # randomly select E, the energy transfer
+    E = Emin + np.random.random(N) * (Emax-Emin)
+    # the final energy
+    Ef = Ei - E
+    # the final velocity
+    from mcni.utils.conversion import e2v
+    vi = e2v(Ei)
+    vf = e2v(Ef)
+    # choose cos(theta) between -1 and 1
+    cos_t = np.random.random(N) * 2 - 1
+    # theta
+    theta = np.arccos(cos_t)
+    # sin(theta)
+    sin_t = np.sin(theta)
+    # phi: 0 - 2pi
+    phi = np.random.random(N) * 2 * np.pi
+    # compute final velocity vector
+    vx,vy,vz = vf*sin_t*np.cos(phi), vf*sin_t*np.sin(phi), vf*cos_t
+    # neutron position, spin, tof are set to zero
+    x = y = z = sx = sy = np.zeros(N, dtype="float64")
+    t = np.ones(N, dtype="float64")
+    t *= L0/vi
+    # probability
+    prob = np.ones(N, dtype="float64") * (vf/vi)
+    # XXX: this assumes a specific data layout of neutron struct
+    n_arr = np.array([x,y,z,vx,vy,vz, sx,sy, t, prob]).T.copy()
+    neutrons.from_npyarr(n_arr)
+    return neutrons