DISCRETE ELEMENT METHOD (DEM) SIMULATION USING OPEN-SOURCE CODES

Transcription

1 DISCRETE ELEMENT METHOD (DEM) SIMULATION USING OPEN-SOURCE CODES Using PYTHON Dr Daniel Barreto 1 Lecturer in Geotechnical Engineering d.barreto@napier.ac.uk July 8 th, 2015 D. Barreto (ENU) DEM-ZU-2015 July 8 th, / 19

2 Lecture Outline 1 PYTHON - YADE s language Python Basics 2 Data types Lists Tuples 3 Control structures 4 Examples of PYTHON functions used in YADE D. Barreto (ENU) DEM-ZU-2015 July 8 th, / 19

3 Python - Basic calculations Python is an interpretative language. You can use PYTHON to run programs from Terminal (command window). Python is also an interactive language that is capable of evaluating arbitrary commands. This is particularly for validation and verification problems. Many people even use PYTHON as a calculator. For example: PYTHON as calculator user@user:~$ python Python (default, Jun , 17:58:13) [GCC 4.8.2] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> D. Barreto (ENU) DEM-ZU-2015 July 8 th, / 19

4 PYTHON - Arithmetic Operators Assuming that a = 10 and b = a+b=30 (Addition) b-a=10 (Subtraction) a*b=200 (Product) b/a=2 (Division) b%a=0 (Module) a**b=10 20 (Power) D. Barreto (ENU) DEM-ZU-2015 July 8 th, / 19

5 Variables - Declaration and printing A typical first program can be created using PYTHON: Hello World! >>> print Hello! D. Barreto (ENU) DEM-ZU-2015 July 8 th, / 19

6 Variables - Declaration and printing A typical first program can be created using PYTHON: Hello World! >>> print Hello! In PYTHON variables (and constants) do not need to be declared. This is an advantage in contrast to other programming languages (i.e. C++ and FORTRAN). For example: Calculations with variables >>> x=2 >>> y=1 >>> x+y D. Barreto (ENU) DEM-ZU-2015 July 8 th, / 19

7 Functions - Declaration In PYTHON it is easy to define and declare functions. It is only necessary to write: def functionname(parameters): Hello World! as a function >>> def functionone():... print Hello... D. Barreto (ENU) DEM-ZU-2015 July 8 th, / 19

8 Functions - Declaration In PYTHON it is easy to define and declare functions. It is only necessary to write: def functionname(parameters): Hello World! as a function >>> def functionone():... print Hello... If the function has several parameters, these are separated by commas. It is not needed to specify the parameter type (also in contrast to other programmming languages). It is very important to maintain the indentation when using PYTHON because functions have no explicit end. There are no brackets or parenthesis as in other languages. The only delimiters used in PYTHON are : and the indentation (i.e. spacing or tabulation). D. Barreto (ENU) DEM-ZU-2015 July 8 th, / 19

9 Indentation and calling functions Code blocks are defined by indentation. A code block can be a conditional ( if ), loop or cycle ( for, while ), etc. Indentation starts and finishes a block. Character spacing is significant and must always be consistent. Functions in PYTHON as in other languages are called by their name and parameters. In this way, functionone() is called as: Calling a function >>> functionone() At this point is good to verify what happens when you call that function (functionone()) D. Barreto (ENU) DEM-ZU-2015 July 8 th, / 19

10 Indentation and calling functions Code blocks are defined by indentation. A code block can be a conditional ( if ), loop or cycle ( for, while ), etc. Indentation starts and finishes a block. Character spacing is significant and must always be consistent. Functions in PYTHON as in other languages are called by their name and parameters. In this way, functionone() is called as: Calling a function >>> functionone() At this point is good to verify what happens when you call that function (functionone()) A further example: Write a function addition() that returns the sum of two integer numbers x and z. Verify that the function works properly. D. Barreto (ENU) DEM-ZU-2015 July 8 th, / 19

11 PYTHON - Data Types Numbers Characters Dictionaries Lists [a, b, c] Tuples (a, b, c) D. Barreto (ENU) DEM-ZU-2015 July 8 th, / 19

12 Lists The most versatile data type in PYTHON. A list can contain any variable type and it os declared as: List declaration >>> list1 = [1,2,3] The first element of that list (and any other) is identified with the index 0. For example: D. Barreto (ENU) DEM-ZU-2015 July 8 th, / 19

13 Lists The most versatile data type in PYTHON. A list can contain any variable type and it os declared as: List declaration >>> list1 = [1,2,3] The first element of that list (and any other) is identified with the index 0. For example: Individual elements of a list >>> list1 = [ DEM,2,3] >>> list1[0] D. Barreto (ENU) DEM-ZU-2015 July 8 th, / 19

14 Lists The most versatile data type in PYTHON. A list can contain any variable type and it os declared as: List declaration >>> list1 = [1,2,3] The first element of that list (and any other) is identified with the index 0. For example: Individual elements of a list >>> list1 = [ DEM,2,3] >>> list1[0] Example: Create the list Crear la lista li = [ One, 1, 1.2] and then verify the content for each of its elements. D. Barreto (ENU) DEM-ZU-2015 July 8 th, / 19

15 Lists Additional elements can be added to existing lists... Adding elements to existing lists >>> list1.append( Three ) >>> list[3] Similarly, individual elements can be removed using the command remove. For example: Removing individual elements from a list >>> list1.remove(2) >>> list1[1] D. Barreto (ENU) DEM-ZU-2015 July 8 th, / 19

16 Tuples Tuples are essentialy and immutable (unchangeable) list. Once a tuple has been created it cannot be changed. Tuples are declared in the same way as lists but using parenthesis () instead of square brackets []. Identification of and access to individual elements of a tuple is made in the same manner as explained for the case of lists. D. Barreto (ENU) DEM-ZU-2015 July 8 th, / 19

17 Tuples Tuples are essentialy and immutable (unchangeable) list. Once a tuple has been created it cannot be changed. Tuples are declared in the same way as lists but using parenthesis () instead of square brackets []. Identification of and access to individual elements of a tuple is made in the same manner as explained for the case of lists. An example... Working with tuples >>> tuple1=(1,2,3) >>> tuple1[0] >>> tuple1.append(4) D. Barreto (ENU) DEM-ZU-2015 July 8 th, / 19

18 Tuples Tuples are essentialy and immutable (unchangeable) list. Once a tuple has been created it cannot be changed. Tuples are declared in the same way as lists but using parenthesis () instead of square brackets []. Identification of and access to individual elements of a tuple is made in the same manner as explained for the case of lists. An example... Working with tuples >>> tuple1=(1,2,3) >>> tuple1[0] >>> tuple1.append(4) What do you expect to have when executing the code above? D. Barreto (ENU) DEM-ZU-2015 July 8 th, / 19

19 PYTHON - Comparison operators Assuming that a = 10 and b = a==b False (Equality) a!=b True (Inequality) a>b False (Greater than) a<b True (Lower than) a>=b False (Greater or equal than) a<=b True (Lower or equal than) D. Barreto (ENU) DEM-ZU-2015 July 8 th, / 19

20 PYTHON - Logical operators Assuming that a = 10 and b = a and b True Both arguments must be true for the condition to be true a or b True If any of the argumets is different from zero, the condition is true not(a and b) False If one condition is true, the operator not makes it false D. Barreto (ENU) DEM-ZU-2015 July 8 th, / 19

21 if A control structure, whether it is a conditional (if) or a loop/cycle (for) has a very simple syntaxis that follows the basic principles for PYTHON The if conditional >>> def if1(x,y):... if x == 1:... print Bien... if x >= 2:... z = x+y... print z Let s verify this works using the following commands: Verifying... >>> if1(1,2) >>> if1(2,1) D. Barreto (ENU) DEM-ZU-2015 July 8 th, / 19

22 for A control structure, whether it is a conditional (if) or a loop/cycle (for) has a very simple syntaxis that follows the basic principles for PYTHON The for loop/cycle >>> def for1():... for x in range(5):... print x D. Barreto (ENU) DEM-ZU-2015 July 8 th, / 19

23 for A control structure, whether it is a conditional (if) or a loop/cycle (for) has a very simple syntaxis that follows the basic principles for PYTHON The for loop/cycle >>> def for1():... for x in range(5):... print x Example: Create a list with three integer numbers. Then define a function that prints each of these elements and the sum of them. Use a conditional structure that verifues and prints if the sum is greater or lower than 10. D. Barreto (ENU) DEM-ZU-2015 July 8 th, / 19

24 More PYTHON details Dive Into Python. A Book By Mark Pilgrim. D. Barreto (ENU) DEM-ZU-2015 July 8 th, / 19

25 Outputting data A function to output macro-scale data to a text file def plotadddata(): plot.adddata( sxx=utils.getstress()[0,0], syy=utils.getstress()[1,1], szz=utils.getstress()[2,2], poros=porosity(), t=o.time ) plot.savedatatxt( macrofile,vars=( t, sxx, syy, szz, poros )) D. Barreto (ENU) DEM-ZU-2015 July 8 th, / 19

26 A more general output function Formatted output... def fabric(): filename= fabric +str(o.iter) f = open(filename, w ) f.write( id1 id2 x_cp y_cp z_cp n_x n_y n_z ) for i in O.interactions: if not i.isreal: continue tacts = i.geom.contactpoint nmls = i.geom.normal f.write( %-16d %-16d %-16g %-16g %-16g %-16g %-16g %-16g\n %(i.id1, i.id2,tacts[0],tacts[1],tacts[2],nmls[0],nmls[1],nmls[2],)) f.close D. Barreto (ENU) DEM-ZU-2015 July 8 th, / 19

27 Servo-control for a drained triaxial test def servo(): gain=0.001 tol=0.1 sy_req=-250. sz_req=-250. sr_x=-.1 sr_y=0. sr_z=0. sy_curr=utils.getstress()[1,1] sz_curr=utils.getstress()[2,2] sry_curr=o.cell.velgrad[1,1] srz_curr=o.cell.velgrad[2,2] if fabs(sy_curr-sy_req)>=tol: sr_y=sry_curr+gain*(sy_req-sy_curr) else: sr_y=sry_curr if fabs(sz_curr-sz_req)>=tol: sr_z=srz_curr+gain*(sz_req-sz_curr) else: sr_z=srz_curr O.cell.velGrad=Matrix3(sr_x,0,0,0,sr_y,0,0,0,sr_z) D. Barreto (ENU) DEM-ZU-2015 July 8 th, / 19