From 364901cc22e47740beae39ee80c3c15be38c4c2b Mon Sep 17 00:00:00 2001
From: Andreas Dutzler <a.dutzler@gmail.com>
Date: Wed, 15 Mar 2023 22:49:26 +0100
Subject: [PATCH 01/13] Update model.py

---
 src/trusspy/model.py | 38 ++++++++------------------------------
 1 file changed, 8 insertions(+), 30 deletions(-)

diff --git a/src/trusspy/model.py b/src/trusspy/model.py
index 30ed9b7..ae2e448 100644
--- a/src/trusspy/model.py
+++ b/src/trusspy/model.py
@@ -6,7 +6,6 @@
 """
 
 import copy
-import os
 import sys
 import time
 from subprocess import run as sp_run
@@ -137,14 +136,11 @@ def __init__(self, file=None, log=2, logfile=False, logfile_name="analysis"):
         self.Boundaries = BoundaryHandler()
         self.ExtForces = ExternalForceHandler()
         self.Settings = SettingsHandler()
-        # self.Results = ResultHandler()
-        # self.Analysis = Analysis()
 
         self.Settings.log = log
 
         if log > 1:
             print("    - finished.\n")
-        # if log > 1: print('-'*88+'\n')
 
         if file is not None:
             if log > 1:
@@ -196,10 +192,9 @@ def __init__(self, file=None, log=2, logfile=False, logfile_name="analysis"):
 
             if log > 1:
                 print("    - Import finished.\n")
-            # if log > 1: print('-'*88)
 
     def build(self):
-        """build Model (r,U,K,...) with Model data and dimensions."""
+        "Build Model (r,U,K,...) with Model data and dimensions."
 
         self.Results = ResultHandler()
         self.Analysis = Analysis()
@@ -228,8 +223,7 @@ def build(self):
         if 2 in self.Elements.mat_type:
             self.Settings.nstatev = 2
 
-        # node properties
-        # n----pro-------
+        # (n)ode (pro)perties
         #
         #      active = free  = 1
         #    inactive = fixed = 0
@@ -374,10 +368,6 @@ def run(self):
         self.Analysis.Vred = np.append(self.Analysis.Ured, 0)
         self.Analysis.lpf = 0
 
-        # init LPF
-        # self.Settings.lpf = self.Settings.dlpf
-        # self.Analysis.lpf = self.Settings.dlpf
-
         for step in range(self.Settings.nsteps):
 
             # maximum number of increment and maximum value per step
@@ -401,9 +391,6 @@ def run(self):
 
                 print(r"$$\text{Value}_i = \left|\frac{D_x}{D_{x,max}}\right|_i$$")
 
-            # get reduced external force vector
-            # f0red = self.ExtForces.forces[:,3*(step):3*(step+1)].flatten()[self.Analysis.DOF1]
-            # self.Analysis.f0red = f0red.reshape(len(f0red),1)
             self.Analysis.ExtForces = copy.deepcopy(self.ExtForces)
 
             f0_const = np.zeros_like(
@@ -544,15 +531,11 @@ def run(self):
                 )
 
     def stiffness(self, Ured, analysis=None):
-        "Method for Stiffness Matrix."
-
-        # In a future version this function should be implemented in Stiffness class part of the Model or Results
-        # self.Stiffness(reduced=True)
-
-        # it re-shapes stiffness matrix to
-        # K(nnodes,nnodes,ndim,ndim) --> K(nnodes*ndim,nnodes*nim)
-        # and returns a view on the reduced (active part of the) matrix
-        # K(nnodes*ndim,nnodes*nim)[active DOF rows][:,active DOF columns]
+        """Method for evaluating the stiffness matrix. It re-shapes the stiffness matrix
+        to ``K(nnodes,nnodes,ndim,ndim) --> K(nnodes*ndim,nnodes*nim)`` and returns a
+        view on the reduced (active part of the) matrix
+        ``K(nnodes*ndim,nnodes*nim)[active DOF rows][:,active DOF columns]``.
+        """
 
         if analysis is not None:
             self.Analysis = analysis
@@ -577,7 +560,7 @@ def stiffness(self, Ured, analysis=None):
         return self.Analysis.Kred
 
     def equilibrium(self, Ured, U0red, stage="G", analysis=None, statev_write=False):
-        """Method to generate equilibrium for given displacements and external forces."""
+        "Method to generate equilibrium for given displacements and external forces."
 
         if analysis is not None:
             self.Analysis = analysis
@@ -585,7 +568,6 @@ def equilibrium(self, Ured, U0red, stage="G", analysis=None, statev_write=False)
         # remove last entry in Vred to get only displacement DOFs
         if len(Ured) > self.ndof1:
             lpf = Ured[-1]
-            lpf0 = U0red[-1]
             Ured = Ured[: self.ndof1]
             U0red = U0red[: self.ndof1]
         else:
@@ -642,14 +624,11 @@ def equilibrium(self, Ured, U0red, stage="G", analysis=None, statev_write=False)
                 rnodes[n] = self.Analysis.r[np.where(self.Nodes.labels == node)][0]
 
             mat_type = self.Elements.get_material_type(e)
-            # elem_type = self.Elements.get_element_type(e)
 
             if mat_type == 1:
                 umat = umat_el
             elif mat_type == 2:
                 umat = umat_elplast_iso
-            elif mat_type == 3:
-                umat = umat_elplast_kiniso
 
             self.Analysis, state_v = truss(
                 e,
@@ -668,7 +647,6 @@ def equilibrium(self, Ured, U0red, stage="G", analysis=None, statev_write=False)
                 self.Analysis,
             )
             if statev_write and self.Settings.nstatev > 0:
-                # print('write state-variable for element', int(e), state_v[0])
                 self.Analysis.state_v = state_v
                 self.Analysis.lpf = lpf
                 self.Analysis.Vred = np.append(Ured, lpf)

From 72f3f0cd8c5000cef2b6fe7cd3e29a3664f5d60c Mon Sep 17 00:00:00 2001
From: Andreas Dutzler <a.dutzler@gmail.com>
Date: Wed, 15 Mar 2023 22:49:28 +0100
Subject: [PATCH 02/13] Update tpsolver.py

---
 src/trusspy/solvers/tpsolver.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/trusspy/solvers/tpsolver.py b/src/trusspy/solvers/tpsolver.py
index 15e8211..4b5922d 100644
--- a/src/trusspy/solvers/tpsolver.py
+++ b/src/trusspy/solvers/tpsolver.py
@@ -1,8 +1,8 @@
 # -*- coding: utf-8 -*-
 """
-Created on Mon Jul 30 17:36:41 2018
-
-@author: adutz
+title: TrussPy - Truss Solver for Python
+author: Andreas Dutzler
+year: 2023
 """
 
 import copy

From edf50c515edb134baf51df0c341c99f2057a72d1 Mon Sep 17 00:00:00 2001
From: Andreas Dutzler <a.dutzler@gmail.com>
Date: Wed, 15 Mar 2023 22:53:52 +0100
Subject: [PATCH 03/13] shorten printed header in `Model`

---
 src/trusspy/model.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/src/trusspy/model.py b/src/trusspy/model.py
index ae2e448..aff5791 100644
--- a/src/trusspy/model.py
+++ b/src/trusspy/model.py
@@ -117,10 +117,7 @@ def __init__(self, file=None, log=2, logfile=False, logfile_name="analysis"):
 TrussPy - Truss Solver for Python
           Version {__version__}
 
-Author: Dutzler A.
-        Graz University of Technology, 2018
-        
-TrussPy Copyright (C) 2023 Andreas Dutzler
+Dutzler Andreas, Graz University of Technology, 2023
         """
             )
 

From e0b3dfb5067d2831dd4a69018c2a901f017bf251 Mon Sep 17 00:00:00 2001
From: Andreas Dutzler <a.dutzler@gmail.com>
Date: Wed, 15 Mar 2023 22:53:56 +0100
Subject: [PATCH 04/13] Delete result.py

---
 src/trusspy/core/result.py | 124 -------------------------------------
 1 file changed, 124 deletions(-)
 delete mode 100644 src/trusspy/core/result.py

diff --git a/src/trusspy/core/result.py b/src/trusspy/core/result.py
deleted file mode 100644
index 0468c02..0000000
--- a/src/trusspy/core/result.py
+++ /dev/null
@@ -1,124 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-title: TrussPy - Truss Solver for Python
-author: Andreas Dutzler
-year: 2023
-"""
-
-import numpy as np
-
-
-class Result:
-    """Result class.
-
-    Attributes
-    ----------
-    U : ndarray
-        2d-array with total displacement vector
-        `U.shape = (nnodes, ndim)`. To get Ux,Uy,Uz of node i type: `U[i]`
-
-    r : ndarray
-        2d-array with internal force vector
-        `r.shape = (nnodes, ndim)`. To get rx,ry,rz of node i type: `r[i]`
-
-    g : ndarray
-        2d-array with equilibrium vector
-        `g.shape = (nnodes, ndim)`. To get gx,gy,gz of node i type: `g[i]`
-
-    stretch : ndarray
-        2d-array with stretch vector
-        `stretch.shape = (nelems, 1)`. To get stretch of element i
-        type: `stretch[i]`
-
-    element_force : ndarray
-        2d-array with element force vector
-        `element_force.shape = (nelems, 1)`. To get element_force of element i
-        type: `element_force[i]`
-
-    K : ndarray
-        4d-array with stiffness matrix
-        `K.shape = (nnodes,nnodes,ndim,ndim)`. To get K with shape (ndim,ndim)
-        between node i and node j type K[i,j].
-
-    state_v : ndarray
-        state variable vector
-
-
-
-    Todo
-    ----
-    * simplify reduced set with DOF1 read/write options
-    """
-
-    def __init__(self):
-        self.U = None
-        self.r = None
-        self.g = None
-        self.stretch = None
-        self.element_force = None
-        self.K = None
-        self.state_v = None
-
-    def build(self, nnodes, nelems, ndim, DOF0, DOF1, nstatev=0):
-        """Build/initialize result class with given dimensions.
-
-        Parameter
-        ---------
-        nnodes : int
-            Number of nodes
-        nelems : int
-            Number of elements
-        ndim : int
-            Dimension of analysis
-        DOF0 : int
-            indices of inactive degree of freedoms
-            (generated with flattened degree of freedoms)
-        DOF1 : int
-            indices of active degree of freedoms
-            (generated with flattened degree of freedoms)
-
-        Raises
-        ----------
-        ValueError : Result is not empty and can't be built.
-            Dimensions already set.
-
-        Todo
-        ----
-        * simplify reduced slice read/write operations
-        """
-        if self.U is None:
-            self.U = np.zeros((nnodes, ndim))
-            self.U0 = np.zeros((nnodes, ndim))
-            self.r = np.zeros((nnodes, ndim))
-            self.g = np.zeros((nnodes, ndim))
-            self.K = np.zeros((nnodes, nnodes, ndim, ndim))
-            # self.dlamdU = np.zeros((nnodes,ndim))
-            self.stretch = np.zeros((nelems, 1))
-            self.element_force = np.zeros((nelems, 1))
-            self.element_stress0 = np.zeros((nelems, 1))
-            self.element_stress = np.zeros((nelems, 1))
-            self.DOF0 = DOF0
-            self.DOF1 = DOF1
-            self.Ured = self.get_U(flat=True)[DOF1]
-            self.rred = self.get_r(flat=True)[DOF1]
-            if nstatev > 0:
-                self.state_v = np.zeros((nelems, nstatev))
-
-        else:
-            raise ValueError("Displacements or Residuals already loaded.")
-
-    def get_U(self, flat=False, red=False):
-        if flat:
-            return self.U.flatten()
-        elif red:
-            return self.Ured
-        else:
-            return self.U
-
-    def get_r(self, flat=False, red=False):
-        if flat:
-            return self.r.flatten()
-        elif red:
-            return self.rred
-        else:
-            return self.r

From 908a881df1ad77bf35def3d7fb1cf401db20b0d4 Mon Sep 17 00:00:00 2001
From: Andreas Dutzler <a.dutzler@gmail.com>
Date: Wed, 15 Mar 2023 22:55:48 +0100
Subject: [PATCH 05/13] Update analysis.py

---
 src/trusspy/core/analysis.py | 29 +++++------------------------
 1 file changed, 5 insertions(+), 24 deletions(-)

diff --git a/src/trusspy/core/analysis.py b/src/trusspy/core/analysis.py
index 49f8be8..949bd66 100644
--- a/src/trusspy/core/analysis.py
+++ b/src/trusspy/core/analysis.py
@@ -16,64 +16,48 @@ class Analysis:
     U : None
         placeholder for 2d-array with total displacement vector at the end of the inc.
         `U.shape = (nnodes, ndim)`. To get Ux,Uy,Uz of node i type: `U[i]`
-
     U0 : None
-        placeholder for 2d-array with total displacement vector at the beginning of the inc.
-        `U0.shape = (nnodes, ndim)`. To get U0x,U0y,U0z of node i type: `U0[i]`
-
+        placeholder for 2d-array with total displacement vector at the beginning of the
+        inc. `U0.shape = (nnodes, ndim)`. To get U0x,U0y,U0z of node i type: `U0[i]`
     r : None
         placeholder for 2d-array with internal force vector
         `r.shape = (nnodes, ndim)`. To get rx,ry,rz of node i type: `r[i]`
-
     g : None
         placeholder for 2d-array with equilibrium vector
         `g.shape = (nnodes, ndim)`. To get gx,gy,gz of node i type: `g[i]`
-
     K : None
         placeholder for 4d-array with stiffness matrix
         `K.shape = (nnodes,nnodes,ndim,ndim)`. To get K with shape (ndim,ndim)
         between force of node i w.r.t. displacement of node j type K[i,j].
-
     stretch : None
         placeholder for 2d-array with stretch vector
         `stretch.shape = (nelems, 1)`. To get stretch of element i
         type: `stretch[i]`
-
     element_force : None
         placeholder for 2d-array with element force vector
         `element_force.shape = (nelems, 1)`. To get element_force of element i
         type: `element_force[i]`
-
     element_stress : None
         placeholder for 2d-array with element stress vector
         `element_stress.shape = (nelems, 1)`. To get element_stress of element i
         type: `element_stress[i]`
-
     element_stress0 : None
-        placeholder for 2d-array with element stress vector at the beginning of the increment
-        `element_stress0.shape = (nelems, 1)`. To get element_stress0 of element i
-        type: `element_stress0[i]`
-
+        placeholder for 2d-array with element stress vector at the beginning of the
+        increment ``element_stress0.shape = (nelems, 1)``. To get element_stress0 of
+        element ``i`` type: ``element_stress0[i]``.
     DOF0 : None
         placeholder for indices of inactive (locked) degree of freedoms
-
     DOF1 : None
         placeholder for indices of active (free) degree of freedoms
-
     Ured : None
         placeholder for reduced dispaclement vector
         (only active components of U)
-
     Vred : None
         placeholder for reduced dispaclement vector
         (only active components of V)
-
     state_v : None
         placeholder for state variable vector
 
-    Todo
-    ----
-    * simplify reduced set with DOF1 read/write options
     """
 
     def __init__(self):
@@ -122,9 +106,6 @@ def build(self, nnodes, nelems, ndim, DOF0, DOF1, nstatev=0):
         ValueError : Result is not empty and can't be built.
             Dimensions already set.
 
-        Todo
-        ----
-        * simplify reduced slice read/write operations
         """
         if self.U is None:
             self.step = 1

From 985f8244d3ca07d3be6f381afc4db6391cd878d6 Mon Sep 17 00:00:00 2001
From: Andreas Dutzler <a.dutzler@gmail.com>
Date: Wed, 15 Mar 2023 23:01:32 +0100
Subject: [PATCH 06/13] simplify core components

---
 src/trusspy/core/boundary.py       |  3 --
 src/trusspy/core/element.py        | 52 ++++++++++++------------------
 src/trusspy/core/external_force.py | 25 +++++++-------
 src/trusspy/core/node.py           | 24 +++++++-------
 4 files changed, 46 insertions(+), 58 deletions(-)

diff --git a/src/trusspy/core/boundary.py b/src/trusspy/core/boundary.py
index ea288c3..356d0e8 100644
--- a/src/trusspy/core/boundary.py
+++ b/src/trusspy/core/boundary.py
@@ -27,9 +27,6 @@ class BoundaryU:
         Array of boundary components: `array([U1, U2, U3])`.
         Set 1 for active (free) DOF and 0 for inactive (locked) DOF.
 
-    Todo
-    ----
-    - rename to DOFState or something similar
     """
 
     def __init__(self, node, values):
diff --git a/src/trusspy/core/element.py b/src/trusspy/core/element.py
index aa028d6..37f144b 100644
--- a/src/trusspy/core/element.py
+++ b/src/trusspy/core/element.py
@@ -11,24 +11,6 @@
 class Element:
     """Element class.
 
-    Parameter
-    ---------
-    label : int
-        Element ID number
-    conn : array_like
-        List of Element connectivity : `[Node 1, Node 2]`
-
-    elem_type : int, optional
-        Element Type. (default is 1 for truss)
-    mat_type : int, optional
-        Material Type. (default is 1 for linear-elastic)
-    material_properties : array_like, optional
-        List with material parameters,
-        e.g. [Young's modulus, Thermal expansion coefficient] (default is [])
-    geometric_properties : array_like, optional
-        List with geometric parameters,
-        e.g. [Section area] (default is [])
-
     Attributes
     ----------
     label : int
@@ -46,11 +28,6 @@ class Element:
         List with geometric parameters,
         e.g. [Section area] (default is [])
 
-    Todo
-    ----
-    + DONE rewrite material parameter storage
-    + DONE material properties: type, mechanical and thermal parameter
-    + DONE geometric porperties: section area
     """
 
     def __init__(
@@ -64,6 +41,27 @@ def __init__(
         mprop=None,
         gprop=None,
     ):
+        """Initialize an instance of the Element class.
+
+        Parameters
+        ----------
+        label : int
+            Element ID number
+        conn : array_like
+            List of Element connectivity ``[Node 1, Node 2]``.
+        elem_type : int, optional
+            Element Type (default is 1 for "truss").
+        mat_type : int, optional
+            Material Type (default is 1 for "linear-elastic").
+        material_properties : array_like, optional
+            List with material parameters,
+            e.g. ``[Young's modulus, Thermal expansion coefficient]`` (default is
+            [np.nan]).
+        geometric_properties : array_like, optional
+            List with geometric parameters,
+            e.g. ``[Section area]`` (default is [np.nan]).
+
+        """
 
         self.label = label
         self.conn = np.array(conn)
@@ -89,11 +87,3 @@ def __init__(
             self.geometric_properties = gprop
         else:
             self.geometric_properties = geometric_properties
-
-    # def get_NE(self):
-    #    """get end node of element"""
-    #    return self.conn[1]
-
-    # def get_NA(self):
-    #    """get begin node of element"""
-    #    return self.conn[0]
diff --git a/src/trusspy/core/external_force.py b/src/trusspy/core/external_force.py
index 7b1a8a9..28c16ee 100644
--- a/src/trusspy/core/external_force.py
+++ b/src/trusspy/core/external_force.py
@@ -11,25 +11,26 @@
 class ExternalForce:
     """External Force class.
 
-    Parameter
-    ---------
-    node : int
-        Node ID number
-    force : array_like
-        List of Force components: `[F1, F2, F3]`
-
     Attributes
     ----------
     node : int
-        Node ID number
+        The node ID number,
     force : ndarray
-        Array containing Force components `array([F1, F2, F3])`
+        Array containing force components ``array([F1, F2, F3])``.
 
-    TODO's
-    ------
-    - add steps/stages by extending `force`
     """
 
     def __init__(self, node, force):
+        """External Force class.
+
+        Parameters
+        ----------
+        node : int
+            The node ID number.
+        force : array_like
+            List of Force components ``[F1, F2, F3]``.
+
+        """
+
         self.node = node
         self.force = np.array(force, dtype=float)
diff --git a/src/trusspy/core/node.py b/src/trusspy/core/node.py
index e0b3113..e875769 100644
--- a/src/trusspy/core/node.py
+++ b/src/trusspy/core/node.py
@@ -11,26 +11,26 @@
 class Node:
     """Node class.
 
-    Parameter
-    ---------
-    label : int
-        Node ID number
-    coord : array_like
-        List of node coordinates: `[X, Y, Z]`
-
     Attributes
     ----------
     label : int
         Node ID number
     coord : ndarray
-        List of node coordinates: `[X, Y, Z]`
+        List of node coordinates: ``[X, Y, Z]``
 
-    Todo
-    ----
-    - add undeformed/deformed coordinates (useful?)
-    - copy deformed coordinates to result class at the end of each increment
     """
 
     def __init__(self, label, coord):
+        """Node class.
+
+        Parameters
+        ----------
+        label : int
+            Node ID number
+        coord : array_like
+            List of node coordinates: ``[X, Y, Z]``
+
+        """
+
         self.label = label
         self.coord = np.array(coord)

From 9ac7a35cdc4423444a72f9789d07c09e98335a47 Mon Sep 17 00:00:00 2001
From: Andreas Dutzler <a.dutzler@gmail.com>
Date: Wed, 15 Mar 2023 23:05:10 +0100
Subject: [PATCH 07/13] simplify handlers

---
 src/trusspy/elements/element_definition.py |  1 -
 src/trusspy/handlers/handler_boundary.py   |  5 -----
 src/trusspy/handlers/handler_element.py    | 13 -------------
 3 files changed, 19 deletions(-)

diff --git a/src/trusspy/elements/element_definition.py b/src/trusspy/elements/element_definition.py
index da017bb..5996401 100644
--- a/src/trusspy/elements/element_definition.py
+++ b/src/trusspy/elements/element_definition.py
@@ -39,7 +39,6 @@ def truss(
     dx0 = dX + dU0
 
     # elemental normal vector in deformed configuration
-    n0 = dx / np.linalg.norm(dx0)
     n = dx / np.linalg.norm(dx)
 
     # elemental length in undeformed and deformed configuration
diff --git a/src/trusspy/handlers/handler_boundary.py b/src/trusspy/handlers/handler_boundary.py
index c7195a9..ffe6d5e 100644
--- a/src/trusspy/handlers/handler_boundary.py
+++ b/src/trusspy/handlers/handler_boundary.py
@@ -94,8 +94,3 @@ def add_bounds_T(self, BB):
         # add list of thermal boundaries
         for B in BB:
             self.add_bound_T(B)
-
-    # def DOFactive(self,ndof):
-    #    # 0 = gesperrt
-    #    O = np.ones(ndof)
-    #    np.where(self.Uvalues, 0 or False)
diff --git a/src/trusspy/handlers/handler_element.py b/src/trusspy/handlers/handler_element.py
index 913de7f..03431db 100644
--- a/src/trusspy/handlers/handler_element.py
+++ b/src/trusspy/handlers/handler_element.py
@@ -121,19 +121,6 @@ def add_element_matrix(self, EM, MM, GM, TM):
             self.conns = np.array(EM[:, 2:4])
             self.material_properties = np.vstack((MM[:, 2:12].T, TM[:, 1])).T
             self.geometric_properties = GM[:, 1].reshape(len(GM), 1)
-        else:
-            pass
-            # self.labels = np.append(self.labels,EM[:,0])
-            # self.elem_type = np.append(self.elem_type, np.array(EM[:,1]))
-            # self.mat_type  = np.append( self.mat_type, np.array(EM[:,2]))
-            # self.conns = np.vstack((self.conns,EM[:,3:5]))
-            # self.material = np.append(self.material,EM[:,3])
-            # self.area = np.append(self.area,EM[:,4])
-            # self.alpha = np.append(self.alpha,TM[:,1])
-            # self.material_properties = np.vstack((self.material_properties,
-            #                                      np.vstack((EM[:,5], TM[:,1])).T))
-            # self.geometric_properties = np.append(self.geometric_properties,
-            #                                      EM[:,6].reshape(len(EM),1))
 
     def get_nodes(self, label):
         "choose element label and return connected end node"

From 6d0da12b80459492cc4891236a02a42ed9fb0e79 Mon Sep 17 00:00:00 2001
From: Andreas Dutzler <a.dutzler@gmail.com>
Date: Wed, 15 Mar 2023 23:06:31 +0100
Subject: [PATCH 08/13] Update material_definition.py

---
 src/trusspy/materials/material_definition.py | 17 ++++-------------
 1 file changed, 4 insertions(+), 13 deletions(-)

diff --git a/src/trusspy/materials/material_definition.py b/src/trusspy/materials/material_definition.py
index 4b975f4..346e629 100644
--- a/src/trusspy/materials/material_definition.py
+++ b/src/trusspy/materials/material_definition.py
@@ -20,17 +20,15 @@ def umat_el(e, de, mat_prop, state_v):
 
 
 def umat_elplast_iso(e, de, mat_prop, state_v):
+
     E = mat_prop[0]
     K = mat_prop[1]
     Sy = mat_prop[2]
 
-    # eps_el_0 = stress/E
     eps_pl_0 = state_v[1]
-    # eps_el_0 = e-de-eps_pl_0
-    # eps_0 = eps_el_0 + eps_pl_0
 
     # total strain at time t=t_n+1
-    eps_1 = e  # eps_0+de
+    eps_1 = e
 
     # yield stress at time t=t_n
     if state_v[0] == 0:
@@ -43,27 +41,20 @@ def umat_elplast_iso(e, de, mat_prop, state_v):
     # trial state
     stress_trial = E * (eps_1 - eps_pl_0)
     eps_pl_trial = eps_pl_0
-    # alpha_0 = (stateolde(1)-1)/kmod;
-    # alpha_trial = alpha_0;
     f_trial = abs(stress_trial) - stress_yield_0
 
     if f_trial <= 0:
-        # print('elastic step')
         # elastic strain increment
         stress_1 = stress_trial
-        eps_pl_1 = eps_pl_trial  # eps_pl_1 = eps_pl_0
-        # alpha_1 = alpha_trial; % alpha_1 = alpha_0
+        eps_pl_1 = eps_pl_trial
         dsde = E
-        # elastic tangent
         delta_gamma = 0.0
     else:
-        # print('plastic step')
         # plastic strain increment
         delta_gamma = f_trial / (E + K)
         stress_1 = (1 - (delta_gamma * E) / abs(stress_trial)) * stress_trial
         eps_pl_1 = eps_pl_0 + delta_gamma * np.sign(stress_trial)
-        # alpha_1 = alpha_0 + delta_gamma
-        dsde = E * K / (E + K)  # elastoplastic tangent
+        dsde = E * K / (E + K)
 
     # output (update) stress
     s = stress_1

From e7b1c09b44259d334b8eca84f23213e1f4e75fd9 Mon Sep 17 00:00:00 2001
From: Andreas Dutzler <a.dutzler@gmail.com>
Date: Wed, 15 Mar 2023 23:13:37 +0100
Subject: [PATCH 09/13] simplify tools and solvers

---
 src/trusspy/solvers/tpsolver.py        | 11 ++----
 src/trusspy/solvers/zerosearch.py      | 23 ++-----------
 src/trusspy/tools/helper_functions2.py | 30 +++--------------
 src/trusspy/tools/plot_utilities.py    | 46 ++------------------------
 4 files changed, 11 insertions(+), 99 deletions(-)

diff --git a/src/trusspy/solvers/tpsolver.py b/src/trusspy/solvers/tpsolver.py
index 4b5922d..3ca94bf 100644
--- a/src/trusspy/solvers/tpsolver.py
+++ b/src/trusspy/solvers/tpsolver.py
@@ -79,8 +79,8 @@ def dxmax_control(
     given value `decrease`. Both an increase and decrease is only performed
     inside the interval `minfac*dxmax0 <= dxmax <= maxfac*dxmax0`.
 
-    Parameter
-    ---------
+    Parameters
+    ----------
     dxmax : ndarray
         current incremental limit of system vector x
     dxmax0 : ndarray
@@ -165,7 +165,6 @@ def dxmax_control(
             if j0 == j:
                 if z > 0:
                     pass
-                    # if verbose > 1: print('* increase NR-step size by factor: (inactive due to recycling).'.format(b,3))
                 elif b <= 3:
                     if verbose > 1:
                         print(
@@ -230,10 +229,8 @@ def pathfollow(
         2D Derivative of function w.r.t. `x`
     x : ndarray
         1D Initial solution vector
-
     analysis : trusspy.core.analysis
         Analysis object
-
     dxmax: array_like, optional
         Maximum incremental step in Dx. Several input methods are possible.
         A single float value will assign dxmax to all components of Dx.
@@ -267,7 +264,6 @@ def pathfollow(
         Tolerance for residual of function: `norm(f)` (default is 1e-8)
     xtol : float, optional
         Tolerance for residual of `x`: `norm(x)` (default is 1e-8)
-
     stepcontrol : bool, optional
         Automatic adjustment of incremental stepwidth Dx. Parameters `macfac`,
         `minfac`, `reduce` and `increase` will control the adjustment. All
@@ -285,12 +281,10 @@ def pathfollow(
         newton iterations to achieve convergence will be used. Updating dxmax
         follows `dxmax = dxmax*(1+(nfev-n)/nfev * increase)`.
         (default is 1)
-
     dxtol : float, optional
         Allowed vvershoot factor of control component if solution has
         converged. Will help to speed-up solution and avoid unneccessary re-
         cycles. (default is 1.25)
-
     verbose : int, optional
         Level of information during iterations (default is 0):
         `verbose=0` ... no information,
@@ -303,7 +297,6 @@ def pathfollow(
         `res_x.shape = (incs, len(x)+1)`. Result array `res_x[1]` contains the
         converged solution vector for the first increment. Result component
         res_x[0] contains start solution which is typically zeros.
-
     res_a: Analysis
         Analysis Class (trusspy.core.analysis.Analysis) with converged solution.
     """
diff --git a/src/trusspy/solvers/zerosearch.py b/src/trusspy/solvers/zerosearch.py
index 523da2b..5deb5c3 100644
--- a/src/trusspy/solvers/zerosearch.py
+++ b/src/trusspy/solvers/zerosearch.py
@@ -5,15 +5,10 @@
 year: 2023
 """
 
-import copy
-
-import numpy as np
-from numpy.linalg import norm, solve
-from scipy.sparse import csc_matrix, csr_matrix
+from numpy.linalg import norm
+from scipy.sparse import csr_matrix
 from scipy.sparse.linalg import spsolve
 
-# from numba import jit
-
 
 def newton(f, dfdx, x, nfev=8, ftol=1e-8, xtol=1e-8, verbose=0, *args):
     """Find the roots of a function using the Newton-Rhapson algorithm.
@@ -94,18 +89,7 @@ def newton(f, dfdx, x, nfev=8, ftol=1e-8, xtol=1e-8, verbose=0, *args):
 
     # NEWTON-RHAPSON ITERATIONS
     for n in range(nfev):
-        # dx = -np.linalg.inv(dfdx(x,j,xmax))@f(x,j,xmax)
-
-        # DIRECT SPARSE SOLVER with cs"r" "R"ow optimized sparse matrix
-        # print('x', x)
-        # print('xmax', args[2])
-        # print('f', f(x,*args))
-        # print('dfdx', dfdx(x,*args))
         dx = spsolve(csr_matrix(dfdx(x, *args)), -f(x, *args))
-        # print('dx', dx[:3])
-
-        # DENSE SOLVER
-        # dx = solve(dfdx(x,*args),-f(x,*args))
 
         # UPDATE SOLUTION
         x = x + dx
@@ -115,14 +99,11 @@ def newton(f, dfdx, x, nfev=8, ftol=1e-8, xtol=1e-8, verbose=0, *args):
         x_norm = norm(dx)
 
         if verbose > 0:
-            # print('        {0:2d}          |{1:1.3e} {2:1.3e}|           |           |           |'.format(
-            #      n,f_norm,x_norm))
             print(
                 "|     |  {0:2d}  |       |{1:1.3e}|    |        |    |        |    |        |".format(
                     n + 1, f_norm
                 )
             )
-            # print('+---+------+-------+---------+-----------+-----------+-----------+-----------+')
 
         if f_norm < ftol and x_norm < xtol:
             success = True
diff --git a/src/trusspy/tools/helper_functions2.py b/src/trusspy/tools/helper_functions2.py
index 4acaa3e..da16241 100644
--- a/src/trusspy/tools/helper_functions2.py
+++ b/src/trusspy/tools/helper_functions2.py
@@ -11,11 +11,6 @@
 from matplotlib.patches import FancyArrowPatch
 from mpl_toolkits.mplot3d import proj3d
 
-# from mpl_toolkits.mplot3d import Axes3D
-# from numpy.linalg import norm
-
-# projection : [‘aitoff’ | ‘hammer’ | ‘lambert’ | ‘mollweide’ | ‘polar’ | ‘rectilinear’], optional
-
 
 class Arrow3D(FancyArrowPatch):
     def __init__(self, xs, ys, zs, *args, **kwargs):
@@ -54,7 +49,6 @@ def plot_hist(x, y, nl, xl, yl="LPF", fig=None, ax=None):
     ax.set_ylabel(yl)
     ax.legend()
     plt.gcf().set_size_inches(8, 6)
-    # plt.gca().set_aspect('equal')
     return fig, ax
 
 
@@ -79,7 +73,6 @@ def plot_pth(x, y, inc, yl="LPF", fig=None, ax=None):
     ax.set_xticklabels(xtckl)
     ax.legend()
     plt.gcf().set_size_inches(8, 6)
-    # plt.gca().set_aspect('equal')
     return fig, ax
 
 
@@ -92,19 +85,17 @@ def plot_nodes(X, fig=None, ax=None, view="xz", color="k", size=10):
         i, j = 1, 2
 
     if view == "3d":
-        from mpl_toolkits.mplot3d import Axes3D
 
         if fig is None:
             fig = plt.figure()
         if ax is None:
             ax = fig.add_subplot(111, projection="3d")
-        # ax.scatter(X[:,0],X[:,1],X[:,2],marker='o',s=150,color=color,zorder=30)
+
         ax.plot(X[:, 0], X[:, 1], X[:, 2], color + "o", ms=size, zorder=30)
     else:
         plt.scatter(X[:, i], X[:, j], marker="o", s=15 * size, color=color, zorder=30)
         fig = plt.gcf()
         ax = plt.gca()
-    # plt.axes().set_aspect('equal');
 
     return fig, ax
 
@@ -119,26 +110,23 @@ def plot_force(f0, X, fig=None, ax=None, view="xz", color="C2", scale=0.5):
     if view == "3d":
         i, j, k = 0, 1, 2
     for f0i, Xi in zip(f0, X):
-        # print((f0i==np.zeros(3)).all())
         if ~(f0i == np.zeros(3)).all():
             xx = Xi[i]
             yy = Xi[j]
             if view == "3d":
                 zz = Xi[k]
             if f0i[i] < 0:
-                # xx += -a*f0i[i]
                 pass
             if f0i[j] < 0:
-                # yy += -a*f0i[j]
                 pass
-            # plt.arrow(xx,yy,a*f0i[i],a*f0i[j],color=color,linewidth=4,zorder=3)
+
             if view == "3d":
-                from mpl_toolkits.mplot3d import Axes3D
 
                 if fig is None:
                     fig = plt.figure()
                 if ax is None:
                     ax = fig.add_subplot(111, projection="3d")
+
                 arrow_properties = dict(
                     mutation_scale=20,
                     lw=3,
@@ -153,7 +141,6 @@ def plot_force(f0, X, fig=None, ax=None, view="xz", color="C2", scale=0.5):
                         [xx, xx],
                         [yy, yy],
                         [zz, zz + scale * f0i[k]],
-                        #        color=color,linewidth=3,zorder=20)
                         alpha=0,
                     )
                     a = Arrow3D(
@@ -169,7 +156,6 @@ def plot_force(f0, X, fig=None, ax=None, view="xz", color="C2", scale=0.5):
                         [xx, xx],
                         [yy, yy + scale * f0i[j]],
                         [zz, zz],
-                        #        color=color,linewidth=3,zorder=20)
                         alpha=0,
                     )
                     a = Arrow3D(
@@ -185,7 +171,6 @@ def plot_force(f0, X, fig=None, ax=None, view="xz", color="C2", scale=0.5):
                         [xx, xx + scale * f0i[i]],
                         [yy, yy],
                         [zz, zz],
-                        # color=color,linewidth=3,zorder=20)
                         alpha=0,
                     )
                     a = Arrow3D(
@@ -224,7 +209,7 @@ def plot_force(f0, X, fig=None, ax=None, view="xz", color="C2", scale=0.5):
                         length_includes_head=True,
                     )
                     plt.plot([xx, xx + 0], [yy, yy + scale * f0i[j]], alpha=0)
-    # plt.axes().set_aspect('equal');
+
     return fig, ax
 
 
@@ -259,14 +244,12 @@ def plot_elems(
             else:
                 norm = mpl.colors.Normalize(vmin=contour_lim[0], vmax=contour_lim[1])
             color = colormap(norm(contour[k]))
-            # print(norm(contour[k]),contour[k])
 
             # create a ScalarMappable and initialize a data structure
             s_m = mpl.cm.ScalarMappable(cmap=colormap, norm=norm)
             s_m.set_array([])
 
         if view == "3d":
-            from mpl_toolkits.mplot3d import Axes3D
 
             if fig is None:
                 fig = plt.figure()
@@ -314,7 +297,6 @@ def plot_elems(
             ax=plt.gca(),
         )
         plt.ylabel("CONTOUR = " + clabel)
-        # plt.gca().yaxis.set_label_position("right")
 
     try:
         if len(lim_scale) == 2:
@@ -336,7 +318,6 @@ def plot_elems(
             ax = plot_coord(ax, m)
             zz = np.zeros_like(xx)
             ax.plot_surface(xx, yy, zz, alpha=0.2)
-            # print(ax.elev,ax.azim)
             ax.view_init(20, -40)
 
     except:
@@ -355,8 +336,6 @@ def plot_elems(
             mlimx = (plt.xlim()[1] + plt.xlim()[0]) / 2
             mlimy = (plt.ylim()[1] + plt.ylim()[0]) / 2
             alim = lim_scale * max(alimx, alimy)
-            # lmin, lmax = (lim_scale*min(plt.xlim()[0],plt.ylim()[0]),
-            #              lim_scale*max(plt.xlim()[1],plt.ylim()[1]))
             minx, maxx = (mlimx - alim, mlimx + alim)
             miny, maxy = (mlimy - alim, mlimy + alim)
             if abs(lim_scale) < 100:
@@ -375,7 +354,6 @@ def plot_elems(
                 ax = plot_coord(ax, 1)
             zz = np.zeros_like(xx)
             ax.plot_surface(xx, yy, zz, alpha=0.2)
-            # print(ax.elev,ax.azim)
             ax.view_init(20, -40)
         else:
             plt.gca().set_aspect("equal")
diff --git a/src/trusspy/tools/plot_utilities.py b/src/trusspy/tools/plot_utilities.py
index f80db8c..74081cf 100644
--- a/src/trusspy/tools/plot_utilities.py
+++ b/src/trusspy/tools/plot_utilities.py
@@ -160,16 +160,6 @@ def p_model(
                 view=view,
                 scale=force_scale,
             )
-    #    if 'both' in config:
-    #        fig,ax = plot_nodes(self.Nodes.coords,color='C7',view=view)
-    #        fig,ax = plot_elems(self.Elements.conns,self.Nodes.coords,fig,ax,color='C7',view=view)
-    #        fig,ax = plot_nodes(self.Nodes.coords+self.Results.R[inc].U,fig,ax,color='C2',view=view)
-    #        fig,ax = plot_elems(self.Elements.conns,self.Nodes.coords+self.Results.R[inc].U,
-    #                   fig,ax,color='C0',view=view,contour=con,lim_scale=lim_scale)
-    #        fig,ax = plot_force(self.Results.R[inc].lpf*self.ExtForces.forces[:,3*(step-1):3*step],
-    #                   self.Nodes.coords+self.Results.R[inc].U,
-    #                   fig,ax,view=view,
-    #                   scale=force_scale)
 
     if force_scale is not None and ("deformed" in config or "undeformed" in config):
         # these are matplotlib.patch.Patch properties
@@ -213,8 +203,6 @@ def p_model(
         plt.xlabel(view[0])
         plt.ylabel(view[1])
 
-    # plot_force(self.ExtForces.forces,self.Nodes.coords)
-    # plt.show()
     return fig, ax
 
 
@@ -248,38 +236,12 @@ def p_movie(
 
     for i in incs:
 
-        #        if contour == 'stretch':
-        #            if cbar_limits == 'auto':
-        #                contour_lim = [1-max(abs(self.Results.R[i].stretch[:,0]-1)),1+max(abs(self.Results.R[i].stretch[:,0]-1))]
-        #            else:
-        #                contour_lim = cbar_limits
-        #            con = contour, self.Results.R[i].stretch[:,0], contour_lim
-        #        if contour == 'force':
-        #            if cbar_limits == 'auto':
-        #                contour_lim = [-max(abs(self.Results.R[i].element_force[:,0])),max(abs(self.Results.R[i].element_force[:,0]))]
-        #            else:
-        #                contour_lim = cbar_limits
-        #            con = contour, self.Results.R[i].element_force[:,0], contour_lim
-        #        if contour == 'stress':
-        #            if cbar_limits == 'auto':
-        #                contour_lim = [-max(abs(self.Results.R[i].element_stress[:,0])),max(abs(self.Results.R[i].element_stress[:,0]))]
-        #            else:
-        #                contour_lim = cbar_limits
-        #            con = contour, self.Results.R[i].element_stress[:,0], contour_lim
-        #        if type(contour)==tuple:
-        #            if contour[0] == 'stretch':
-        #                con_data = self.Results.R[i].stretch[:,0]
-        #            elif contour[0] == 'force':
-        #                con_data = self.Results.R[i].element_force[:,0]
-        #            elif contour[0] == 'stress':
-        #                con_data = self.Results.R[i].element_stress[:,0]
-        #            con = contour[0], con_data, contour[1]
-
         self.plot_model(
             config, view, contour, lim_scale, force_scale, nodesize, cbar_limits, i
         )
         plt.savefig("figures/png/fig_{:03d}.png".format(i), dpi=200)
         plt.close("all")
+
     png_to_gif()
 
 
@@ -309,8 +271,7 @@ def p_path(self, nodepath, increment=-1, Y="Displacement X", fig=None, ax=None):
     if fig is None:
         fig, ax = plt.subplots()
     plot_pth(nodepath, yy, increment, Y, fig, ax)
-    # print(np.array(xx),np.array(yy))
-    # plt.show()
+
     return fig, ax
 
 
@@ -354,8 +315,7 @@ def p_history(
     if fig is None:
         fig, ax = plt.subplots()
     plot_hist(xx, yy, nodes[0], X, Y, fig, ax)
-    # print(np.array(xx),np.array(yy))
-    # plt.show()
+
     return fig, ax
 
 

From 3ca3fd6ae0be51fcdca0a7b32b44f89c3ce087b9 Mon Sep 17 00:00:00 2001
From: Andreas Dutzler <a.dutzler@gmail.com>
Date: Wed, 15 Mar 2023 23:20:31 +0100
Subject: [PATCH 10/13] Update model.py

---
 src/trusspy/model.py | 26 ++++++++++++++++----------
 1 file changed, 16 insertions(+), 10 deletions(-)

diff --git a/src/trusspy/model.py b/src/trusspy/model.py
index aff5791..857d171 100644
--- a/src/trusspy/model.py
+++ b/src/trusspy/model.py
@@ -103,6 +103,10 @@ def __init__(self, file=None, log=2, logfile=False, logfile_name="analysis"):
             sys.stdout = open(self.logfile_name + ".md", "w")
 
         if log > 1:
+
+            if self.logfile:
+                print("```")
+
             print(
                 f"""
  _____                  ______      
@@ -120,6 +124,8 @@ def __init__(self, file=None, log=2, logfile=False, logfile_name="analysis"):
 Dutzler Andreas, Graz University of Technology, 2023
         """
             )
+        if self.logfile:
+            print("```")
 
         if log > 1:
             print("")
@@ -504,17 +510,17 @@ def run(self):
 
         if self.logfile:
             sys.stdout = self.stdout
-            sp_run(
-                [
-                    "pandoc",
-                    self.logfile_name + ".md",
-                    "-t",
-                    "latex",
-                    "-o",
-                    self.logfile_name + ".pdf",
-                ]
-            )
             if self.Settings.logpdf:
+                sp_run(
+                    [
+                        "pandoc",
+                        self.logfile_name + ".md",
+                        "-t",
+                        "latex",
+                        "-o",
+                        self.logfile_name + ".pdf",
+                    ]
+                )
                 sp_run(
                     [
                         "pandoc",

From 1c87558a42a1f169c0808b5e445dae5970693197 Mon Sep 17 00:00:00 2001
From: Andreas Dutzler <a.dutzler@gmail.com>
Date: Wed, 15 Mar 2023 23:24:32 +0100
Subject: [PATCH 11/13] Update CHANGELOG.md

---
 CHANGELOG.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index f9db10a..5f0eafc 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,10 @@ All notable changes to this project will be documented in this file. The format
 
 ## [Unreleased]
 
+### Changed
+- Simplify the source code: Remove unused lines of code, To-Do's from function or class docstrings, unify file docstrings.
+- Build HTML and PDF logfiles only if `Settings.logpdf=True` (Pandoc and LaTeX must be installed). Otherwise, only the Markdown logfile `analysis.md` for `Model(logfile=True)` is created (no Pandoc install required).
+
 ## [1.0.2] - 2023-03-13
 
 ### Added

From 8120f75ba7827231be83a6c8268b3f7b7edcadfc Mon Sep 17 00:00:00 2001
From: Andreas Dutzler <a.dutzler@gmail.com>
Date: Wed, 15 Mar 2023 23:26:37 +0100
Subject: [PATCH 12/13] Update CHANGELOG.md

---
 CHANGELOG.md | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5f0eafc..857e2c6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,8 +3,10 @@ All notable changes to this project will be documented in this file. The format
 
 ## [Unreleased]
 
+## [1.0.3] - 2023-03-15
+
 ### Changed
-- Simplify the source code: Remove unused lines of code, To-Do's from function or class docstrings, unify file docstrings.
+- Simplify the source code: Remove unused lines of code, To-Do's from function or class docstrings, unify file docstrings. Trim the header printed by `Model`.
 - Build HTML and PDF logfiles only if `Settings.logpdf=True` (Pandoc and LaTeX must be installed). Otherwise, only the Markdown logfile `analysis.md` for `Model(logfile=True)` is created (no Pandoc install required).
 
 ## [1.0.2] - 2023-03-13

From c8c6030cb6548d9e1063521ee8d9a472abd661e7 Mon Sep 17 00:00:00 2001
From: Andreas Dutzler <a.dutzler@gmail.com>
Date: Wed, 15 Mar 2023 23:26:40 +0100
Subject: [PATCH 13/13] Update __about__.py

---
 src/trusspy/__about__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/trusspy/__about__.py b/src/trusspy/__about__.py
index 7863915..976498a 100644
--- a/src/trusspy/__about__.py
+++ b/src/trusspy/__about__.py
@@ -1 +1 @@
-__version__ = "1.0.2"
+__version__ = "1.0.3"