BatchCalcOrder Created

.dockerignore

@@ -1,25 +1,31 @@
-results
-scr
-old*
-keys
-logs
-data
-backup*
-test_run
-htmlcov
-docs
-bulma
-scratch
+!bin/*.tar.bz2
 *.override.yml
-*__pycache__*
-*.swp
+*.pem
 *.swo
-frontend/tests/keys
-frontend/tests/scr
-frontend/tests/results
+*.swp
+*__pycache__*
 .git
+backup*
 bin/*
-!bin/*.tar.bz2
-gcloud.sh
+bulma
+data
+docs
 frontend/cloud_config.py
-*.pem
+frontend/tests/keys
+frontend/tests/results
+frontend/tests/scr
+gcloud.sh
+htmlcov
+keys
+logs
+npm_modules/node_modules
+npm_packages/css
+npm_packages/css-dist
+npm_packages/js-dist
+npm_packages/node_modules
+old*
+results
+scr
+scratch
+test_run
+firebase

.gitignore

@@ -1,27 +1,34 @@
+!.github
+!bin/*.tar.bz2
+*.override.yml
+*.pem
 *.pyc
-*__pycache__
+*.sqlite3
 *.swp
-calcus/*settings*
+*__pycache__
 *keys/
-*scr/
 *results/
-static/CACHE/
-frontend/migrations/
-*.sqlite3
+*scr/
+scratch/
 .*
-!.github
-*.override.yml
-htmlcov/
-old/
-data/
-logs/
 backup*
-test_run
-docs/build/
-celerybeat-schedule
 bin/*
-!bin/*.tar.bz2
-gcloud.sh
-frontend/cloud_config.py
+calcus/*settings*
+celerybeat-schedule
+data/
+docs/build/
 frontend/cloud_config.json
-*.pem
+frontend/cloud_config.py
+frontend/migrations/
+gcloud.sh
+htmlcov/
+logs/
+npm_packages/css
+npm_packages/css-dist
+npm_packages/js-dist
+npm_packages/node_modules
+old/
+static/CACHE/
+static/testimonials
+test_run
+firebase

Cloud_dockerfile

@@ -8,7 +8,7 @@ ENV CALCUS_CLOUD True
 
 ADD ./cloud_requirements.txt /calcus/cloud_requirements.txt
 RUN pip install -r /calcus/cloud_requirements.txt
-RUN apt update && apt install openbabel postgresql-client dos2unix -y
+RUN apt update && apt install openbabel postgresql-client dos2unix nwchem -y
 
 COPY calcus /calcus/calcus
 COPY frontend /calcus/frontend

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.9 AS calcus_user
+FROM python:3.9-bullseye AS calcus_user
 
 ARG CALCUS_VERSION_HASH
 ENV CALCUS_VERSION_HASH=${CALCUS_VERSION_HASH}
@@ -20,7 +20,10 @@ ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:"/binaries/orca"
 ENV PATH=$PATH:$XTB4STDAHOME/xtb/bin:$XTB4STDAHOME:$EBROOTORCA:$GAUSS_EXEDIR
 ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/binaries/orca:/usr/lib/openmpi/
 
-RUN apt update && apt install openbabel sshpass postgresql-client dos2unix openmpi-bin -y
+RUN apt update && apt install openbabel sshpass postgresql-client dos2unix python3-dev gfortran mpi-default-bin mpi-default-dev -y
+RUN curl -LJO https://github.com/nwchemgit/nwchem/releases/download/v7.2.0-release/nwchem-data_7.2.0-2_all.debian_bullseye.deb
+RUN curl -LJO https://github.com/nwchemgit/nwchem/releases/download/v7.2.0-release/nwchem_7.2.0-2_amd64.debian_bullseye.deb
+RUN dpkg -i nwchem*7.2.0*.deb
 
 ADD ./requirements.txt /calcus/requirements.txt
 RUN pip install -r /calcus/requirements.txt

calcus/settings.py

@@ -67,30 +67,31 @@
 
     stripe.api_key = STRIPE_SECRET_KEY
 
-SUBSCRIPTION_ACADEMIC_MONTHLY = os.getenv("SUBSCRIPTION_ACADEMIC_MONTHLY", "")
-
 # On Google Cloud, the URI of the secret containing the PostgreSQL password (for compute instances)
 POSTGRES_SECRET_URI = os.getenv("POSTGRES_SECRET_URI", "")
 
 POSTGRES_PASSWORD = os.getenv("POSTGRES_PASSWORD")
 POSTGRES_HOST = os.environ.get("POSTGRES_HOST", "postgres")
 POSTGRES_USER = os.environ.get("POSTGRES_USER", "calcus")
 
+"""
 GMAIL_API_CLIENT_ID = os.getenv("CALCUS_EMAIL_ID", "")
 GMAIL_API_CLIENT_SECRET = os.getenv("CALCUS_EMAIL_SECRET", "")
 GMAIL_API_REFRESH_TOKEN = os.getenv("CALCUS_EMAIL_TOKEN", "")
+"""
 
 ALLOWED_HOSTS = [
     "0.0.0.0",
     "0.0.0.0:*",
     "https://calcus.cloud",
+    "https://static.calcus.cloud",
     "calcus.cloud",
-    "localhost",
+    "static.calcus.cloud" "localhost",
     "cloud-compute",
     "cloud-compute:*",
 ]
 
-CSRF_TRUSTED_ORIGINS = ["calcus.cloud"]
+CSRF_TRUSTED_ORIGINS = ["calcus.cloud", "static.calcus.cloud"]
 
 if "CALCUS_CLOUD_INTERNAL" in os.environ:
     ALLOWED_HOSTS.append("*")
@@ -116,14 +117,15 @@
     "django.contrib.sitemaps",
     "axes",
     "bulma",
-    "gmailapi_backend",
+    # "gmailapi_backend",
     "corsheaders",
     #'debug_toolbar',
 ]
 
-if IS_CLOUD:
+if IS_CLOUD or IS_TEST:
     INSTALLED_APPS.append("captcha")
 
+if IS_CLOUD:
     if not DEBUG:
         SECURE_SSL_REDIRECT = True
         SECURE_PROXY_SSL_HEADER = ("HTTP_X_FORWARDED_PROTO", "https")
@@ -164,6 +166,8 @@
         "https://optimize.google.com",
         "https://fonts.googleapis.com",
         "https://storage.googleapis.com",
+        "https://static.calcus.cloud",
+        "https://www.static.calcus.cloud",
     ]
 
 HASHID_FIELD_SALT = os.getenv("CALCUS_HASHID_SALT", "test_salt")
@@ -259,7 +263,15 @@
     EMAIL_BACKEND = "django.core.mail.backends.filebased.EmailBackend"
     EMAIL_FILE_PATH = os.path.join(BASE_DIR, "scratch", "sent_emails")
 else:
-    EMAIL_BACKEND = "gmailapi_backend.mail.GmailBackend"
+    # EMAIL_BACKEND = "gmailapi_backend.mail.GmailBackend"
+    EMAIL_BACKEND = "django.core.mail.backends.smtp.EmailBackend"
+    EMAIL_HOST = "smtp.gmail.com"
+    EMAIL_PORT = 587
+    EMAIL_USE_TLS = True
+    EMAIL_USE_SSL = False
+    EMAIL_HOST_USER = os.getenv("CALCUS_EMAIL_USER")
+    EMAIL_HOST_PASSWORD = os.getenv("CALCUS_EMAIL_PASSWORD")
+
 
 MEDIA_URL = "/media/"
 
@@ -307,7 +319,11 @@
 # Give 600 free CPU-seconds for trial
 TRIAL_DEFAULT_COMP_SECONDS = 600
 FREE_DEFAULT_COMP_SECONDS = 3600
+
+# These allocation amounts shouldn't be used as official reference anymore.
+# The real amounts are parsed from Stripe. These are for testing
 SUBSCRIBER_COMP_SECONDS = 3600 * 60
+SUBSCRIBER_TEAM_COMP_SECONDS = 3600 * 500
 
 if IS_CLOUD:
     PING_SATELLITE = False
@@ -326,30 +342,32 @@
 
     ALLOW_TRIAL = True
 
-    LOCAL_MAX_ATOMS = 200
+    LOCAL_MAX_ATOMS = 50000
 
     LOCAL_ALLOWED_THEORY_LEVELS = [
         "xtb",
         # "semiempirical",
-        # "hf",
+        "hf",
         # "special",  # hf3c, pbeh3c, r2scan3c, b973c
-        # "dft",
+        "dft",
         # "mp2",
         # "cc",
     ]
 
     LOCAL_ALLOWED_STEPS = [
         "Geometrical Optimisation",
         "Conformational Search",
+        "Fast Conformational Search",
         "Constrained Optimisation",
         "Frequency Calculation",
         "TS Optimisation",
         "UV-Vis Calculation",
         "Single-Point Energy",
-        # "Minimum Energy Path",
+        "Minimum Energy Path",
         "Constrained Conformational Search",
         # "NMR Prediction",
-        # "MO Calculation",
+        "MO Calculation",
+        "ESP Calculation",
     ]
 
 else:

calcus/sitemaps.py

@@ -7,7 +7,16 @@ class CalcUSSitemap(sitemaps.Sitemap):
     changefreq = "monthly"
 
     def items(self):
-        return ["frontend:home", "frontend:pricing"]
+        return [
+            ("frontend:home", {}),
+            ("frontend:pricing", {}),
+            ("frontend:register", {}),
+            ("frontend:login", {}),
+            ("frontend:start_trial", {}),
+            ("frontend:learn", {}),
+            ("frontend:learn_keyword", {"keyword": "conformational_search"}),
+        ]
 
-    def location(self, item):
-        return reverse(item)
+    def location(self, item_data):
+        item, kwargs = item_data
+        return reverse(item, kwargs=kwargs)

calcus/urls.py

@@ -27,13 +27,15 @@
 from django.contrib.sitemaps.views import sitemap
 
 from .sitemaps import CalcUSSitemap
+from .views import privacy
 
 sitemaps = {
     "static": CalcUSSitemap,
 }
 
 urlpatterns = [
     path("", include("frontend.urls", namespace="frontend")),
+    path("privacy/", privacy),
     path("accounts/", include("django.contrib.auth.urls")),
     path(
         "sitemap.xml",

calcus/views.py

@@ -45,3 +45,7 @@ class LogoutView(TemplateView):
     def get(self, request, **kwargs):
         logout(request)
         return render(request, self.template_name)
+
+
+def privacy(request):
+    return render(request, "registration/privacy.html")

cloud_requirements.txt

@@ -1,6 +1,6 @@
 basis-set-exchange
 bleach
-ccinput>=1.7.1
+ccinput>=1.9.1
 cryptography
 Django>=3.2.18,<4
 django-appconf==1.0.4
@@ -23,8 +23,11 @@ periodictable
 psutil==5.7.2
 psycopg2
 pysisyphus
+rdkit
 requests
 scipy
+scikit-learn
+spyrmsd
 stripe
 wheel
 xkcdpass

dev-compose.yml

@@ -45,7 +45,7 @@ services:
                         context: .
                         dockerfile: Dockerfile
                         target: calcus_user
-                user: calcus
+                user: "${UID}:${GID}"
                 command: ./scripts/run_celery_main.sh
                 volumes:
                         - ./scr:/calcus/scr
@@ -61,7 +61,7 @@ services:
                         context: .
                         dockerfile: Dockerfile
                         target: calcus_user
-                user: calcus
+                user: "${UID}:${GID}"
                 shm_size: 1gb
                 command: ./scripts/run_celery_comp.sh
                 volumes:
@@ -78,7 +78,7 @@ services:
                         context: .
                         dockerfile: Dockerfile
                         target: calcus_user
-                user: calcus
+                user: "${UID}:${GID}"
                 command: ./scripts/run_cluster_daemon.sh
                 env_file:
                         - ./.env

docker-compose.yml

@@ -40,7 +40,7 @@ services:
                         - web        
         celery_main:
                 image: raphaelrobidas/calcus2:latest
-                user: calcus
+                user: "${UID}:${GID}"
                 command: ./scripts/run_celery_main.sh
                 volumes:
                         - ./scr:/calcus/scr
@@ -54,7 +54,7 @@ services:
                         - redis
         celery_comp:
                 image: raphaelrobidas/calcus2:latest
-                user: calcus
+                user: "${UID}:${GID}"
                 command: ./scripts/run_celery_comp.sh
                 volumes:
                         - ./scr:/calcus/scr

docs/source/software-packages.rst

@@ -70,7 +70,7 @@ The Hamiltonian can be chosen with ``--gfn 2`` (default), ``--gfn 1``, ``--gfn 0
 
 The convergence criteria of geometrical optimisations can be chosen with ``--opt level``, where level is ``crude``, ``sloppy``, ``loose``, ``lax``, ``normal``, ``tight`` (default), ``vtight`` or ``extreme``.
 
-Conformational searches (constrained or not) have several particular options. Faster/cruder sampling procedures can be requested with ``--quick``, ``--squick`` and ``--mquick``. The RMSD threshold for considering conformers as different can be set with ``--rthr X``, where ``X`` is the threshold in Ångström (default of 0.6 in CalcUS). Furthermore, the energy window to consider can be set with ``--ewin X``, where ``X`` is the treshold in kcal/mol (default of 6 in CalcUS).
+Conformational searches (constrained or not) have several particular options. Faster/cruder sampling procedures can be requested with ``--quick``, ``--squick`` and ``--mquick``. The RMSD threshold for considering conformers as different can be set with ``--rthr X``, where ``X`` is the threshold in Ångström (default of 2.0 in CalcUS). Furthermore, the energy window to consider can be set with ``--ewin X``, where ``X`` is the treshold in kcal/mol (default of 6 in CalcUS).
 
 Constrained geometrical optimisations and constrained conformational searches employ a harmonic potential to constrain coordinates (distances, angles, dihedral angles). The force constant of this potential can be chosen with ``--forceconstant X``, where ``X`` is the force constant in Hartree/Bohr². By default, CalcUS uses a force constant of 1.0, which corresponds to a very stiff potential well. In most cases, this high value forces the use of small timesteps in meta-dynamic and molecular dynamic simulations (for constrained conformational searches). If the constrained coordinates do not need to remain exactly constant, the simulations can be accelerated by a smaller force constant.